Hi Rebecca,
1. Can I use JAVA mapping with a main class calling sub classes?
AFAIK SAP PI will call the "execute" class, you main class will not be relevant, although i usually comment it.
2. Does Sequence of the selected JAVA classes matters?
The sequence is not relevant because SAP PI jvm will load them depending your import clauses. The PI only can call the StreamTransformation interface implementation, others class called directly will raise an exception .
Hope this helps.
Regards.