SSL properties are set at the JVM level via system properties. Meaning you can either set them when you run the program (java -D....) Or you can set them in code by doing System.setProperty.

The specific keys you have to set are below:

javax.net.ssl.keyStore- Location of the Java keystore file containing an application process's own certificate and private key. On Windows, the specified pathname must use forward slashes, /, in place of backslashes.

javax.net.ssl.keyStorePassword - Password to access the private key from the keystore file specified by javax.net.ssl.keyStore. This password is used twice: To unlock the keystore file (store password), and To decrypt the private key stored in the keystore (key password).

javax.net.ssl.trustStore - Location of the Java keystore file containing the collection of CA certificates trusted by this application process (trust store). On Windows, the specified pathname must use forward slashes, /, in place of backslashes, \.

If a trust store location is not specified using this property, the SunJSSE implementation searches for and uses a keystore file in the following locations (in order):

1. $JAVA_HOME/lib/security/jssecacerts
2. $JAVA_HOME/lib/security/cacerts

javax.net.ssl.trustStorePassword - Password to unlock the keystore file (store password) specified by javax.net.ssl.trustStore.

javax.net.ssl.trustStoreType - (Optional) For Java keystore file format, this property has the value jks (or JKS). You do not normally specify this property, because its default value is already jks.

javax.net.debug - To switch on logging for the SSL/TLS layer, set this property to ssl.

Just a word of caution. If you are trying to open an existing JKS keystore in Java 9 onwards, you need to make sure you mention the following properties too with value as "JKS":

javax.net.ssl.keyStoreType
javax.net.ssl.trustStoreType

The reason being that the default keystore type as prescribed in java.security file has been changed to pkcs12 from jks from Java 9 onwards.

you can also mention the path at runtime using -D properties as below

-Djavax.net.ssl.trustStore=/home/user/SSL/my-cacerts 
-Djavax.net.ssl.keyStore=/home/user/SSL/server_keystore.jks

In my apache spark application, I used to provide the path of certs and keystore using --conf option and extraJavaoptions in spark-submit as below

--conf 'spark.driver.extraJavaOptions= 
-Djavax.net.ssl.trustStore=/home/user/SSL/my-cacerts 
-Djavax.net.ssl.keyStore=/home/user/SSL/server_keystore.jks' 

First of all, there're two kinds of keystores.

Individual and General

The application will use the one indicated in the startup or the default of the system.

It will be a different folder if JRE or JDK is running, or if you check the personal or the "global" one.

They are encrypted too

In short, the path will be like:

$JAVA_HOME/lib/security/cacerts for the "general one", who has all the CA for the Authorities and is quite important.