When using Amazon Web Service and Tomcat, do you have access to different properties files usually located under the conf folder. Such as catalina.properties, server.properties or does Amazon restrict the modification of those files?
Are you talking about EC2 or Elastic Beanstalk when you say using Amazon Web Service and Tomcat ?
when using EC2
You can view EC2 as really an outsourced server, you're free to run it as you want and amazon will not restrict anything.
You'll be free to install the Tomcat version you want with the Java version you need
when using Elastic Beanstalk
Its the PAAS offering from AWS and as such Amazon will manage Tomcat and all the software for you, you'll be responsible to deliver your application (for Tomcat in form of war file) and you won't get access to the configuration files. There are few configuration parameter you could change but not many.
AWS supports defined version of Java/Tomcat