I need your help here. I'll really appreciate any kind of help as i'm new to this web service stuff.
If you are creating "contract first" web services, there should be no problem at all. If you are generating your contract you can get into trouble.
So stick to contract first and generate booth service implementation and client usage from the contract to be on the "safe" side.
You may have compatibility issues if your axis ws uses rpc/encoded style, since jbossws does not support it because WS-I Basic Profile disallowed it. Rpc/literal and document/literal instead are supported by JBossWS.
Take a look at http://www-128.ibm.com/developerworks/webservices/library/ws-whichwsdl/ for further informations about wsdl styles.