Spring Boot doesn't a microservice make. In fact, you can bundle some distinctly non-micro services into Spring Boot. Spring Boot is just a convenient all-in-one bundling of a webapp server (
e.g., Tomcat) with a webapp so that instead of the usual fuss about installing a webapp server and deploying an app into it, you have an all-in-one module.
However, Spring Boot and Containers are both (and often used together) handy ways of packaging up micro-services for quick and easy deployment.
If you have executable JARs and want to use them via ReST, the first step is then to build webapps based on them. Whether those webapps end up as micro-services of full-blown apps would depend on what your JARs contain.
The preferred way for a Tomcat server to provide custom options to a webapp is to set them up in webapp environment options as part of the deployment of the webapp so that JNDI code within the webapp can find and read them. I've not actually read up on how that would translate into Spring Boot, but I'd expect that the "-D" JVM command line options play a part.