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Difference between connecting to a database using DriverManager and SpringBoot(Hibernate)

There are 2 ways to connect to a database when developing Java apps.
Using DriverManager
Connection conn = DriverManager.getConnection(url, name, password);
// execute the query.
Using application property file in SpringBoot
spring.jpa.hibernate.ddl-auto=none
spring.datasource.url=jdbc:mysql://localhost:5432/db_name
spring.datasource.username=user
spring.datasource.password=password
Now you can use #Entity annotation on your class to put data into database.
My question is how are these 2 ways different. If not how, is SpringBoot method working same as DriverManager in the background.

I assume that by Driver Manager you wanted to made reference to JDBC and by Springboot(Hibernate) you wanted to say JPA.
To simply answer your question, both JDBC and JPA will connect to the driver. Just that if you use JPA this step is made by default without you explicitly coding it.
You can look at JPA as an upper layer of JDBC which handles all the boilerplate code like connecting to the driver.
You can read more about JPA and JDBC here: JPA or JDBC, how are they different?

When you set configuration properties you are just saying to spring: "Hey, i have this properties, can you autoconfigure what i need?". At this point spring at the start of application will use you configuration properties to setup everything you need to connect to your database (using DriverManager or not is not important).
Spring do exactly what you should to do to configure your database connection.
Remember that in 99% of cases you can't write better code than spring do. So, use spring properties

h2 database and sql server in spring boot

I was asked this question by a colleague, and I am unable to answer it:
I have an in memory database (h2), and I have a SQL database server which our app needs to talk too. But due to the two different SQL dialects we are now wondering how do we get around the issue by doing the least amount of work?
This to be done in spring boot. I am aware of how to connect to the h2 database and SQL database server, but I am unsure on the rest.

If everything is setup by Spring, you should not be worried about the 2 different SQL dialects. Just be sure that spring.jpa.database is set to default to let Spring autodetect the right dialect for each datasource.
Here's a link that explain how to use/initialize two datasource in a Spring Boot projet if you need some more information.

Ready made beans to connect MySQL by jdbc?

Can I just load com.mysql.jdbc.jdbc2.optional.MysqlConnectionPoolDataSource class as a bean in Spring? What are this class API? Where it can be found?
I can only find samples of JNDI usage.
Are there any ready-made beans to have such properties like driverName, connectionString userName, password and which allow to issue SQL statements?
EDIT 1
Sorry forgot to say that I need solution except with DriverManagerDataSource because it is said manual it is very basic and not suitable for J2EE containers.

Section 13.3.1 of the Spring User Guide, titled Data access with JDBC, shows how to create a bean to access a database. You specify username, password, driver class, url, etc., to create a bean representing a DataSource.
You can use any data source class here, not only the DriverManagerDataSource shown in the example at the link above. For example, we deploy to Tomcat so I use org.apache.tomcat.jdbc.pool.DataSource as our data source. If you're using Tomcat you can read more about that pool here: The Tomcat JDBC Connection Pool

Some confusion surrounding JDBC Resources and JDBC Connection pools Glassfish

I am about to make a connection to my database and I am using EJB and JPA. I have recently started doing these technologies so I have some problems understand it all at this point:)
I know that the persistence.xml is needed in order to use JPA. It is the file where I configure how to connect to the database, that I know. However it seems like there are multiple ways of doing it.
What would be the difference (or when should I even use the one alternative over the other?) of defining properties such as username, database, password etc. in the persistence.xml file and in Glassfish? Advantages/disadvantages if any.
Underneath on the image I posted I have JDBC Resources and JDBC Connection Pools. I am a litte confused about the terminology of the two. Why don't we add properties such as username, database, password and so on in the JDBC Resources? Could someone explain the difference between them and what they mean?
JDBC Resources
A JDBC resource (data source) provides applications with a means of
connecting to a database. Typically, the administrator creates a JDBC
resource for each database accessed by the applications deployed in a
domain. (However, more than one JDBC resource can be created for a
database.)
http://download.oracle.com/docs/cd/E19316-01/820-4335/ablih/index.html
I think it strange that we add such properties on the pool but not in the resource, but I probably misunderstand the concepts.

In the "JDBC connection pools" you can create container managed JDBC data sources (with connection pooling capabilities). The data source needs to know about at least the JDBC driver, the JDBC URL, username and password.
In the "JDBC resources" you can bind those container managed JDBC data sources to one or more JNDI names so that they are by JNDI available to the deployed web application.
In the persistence.xml you can specify whether to use a local data source or to use a container managed data source. If you want to use a container managed data source, then you should specify its JNDI name. Using a container managed data source has the advantage that you can share a single data source among multiple web applications. In case of JPA, it has also the advantage that you can make use of JTA (container managed transactions) so that you don't need to call transaction.begin(), commit(), rollback() etc in every method.

where to store database string connection in java web app?

I'm about to begin my first project with java
Let me tell how I used to handle these things...
So far now, I've been workin on asp with a com+ componente made with VB6.
The component is registered via the com+ administration console with a domain user, something lile my_company_domain\my_app_account
The components reads the configuration from an udl file, configured to access the DB with integrated security.
I invoke the componente from asp with server.createobject, the component runs with the specified domain account, and so every DB access runs with this account...
What I like from this approach is the following:
use of integrated security - no sql users
no need to recompile anything to change db (edit udl file) or domain account (edit com+ component configuration)
pooled connections (as I'm always using the same connection string)
production staff can alter the configuration without leaving the account password on a text file
...
well, what would be the best way to achieve something like this on java???
I've already saw something about Commons-DBCP, is it possible to use integrated security with this???
thanks a lot...
--
added in response to a comment
by integrated security I mean I only have to configure a domain account, and that's it, I use no sql server accounts, just the account under which the VB6 com+ component is run.
Ok, maybe that's not the appropiate term, but I hope you get the idea...

Configure DataSource & ConnectionPool on app-server side.
Obtain DataSource from JNDI environment from your web-application.