Hi zarana,
This might be a trivial answer to your question.

Can you create a batch file (or Unix script) that executes testrunner separately for each endpoint (specified using
-e command-line switch)?
soapUI. when run in standard mode or when test runner is run, does not have the facility to specify run more than one test suite.
However, you could achieve something like that by executing Groovy script placed as the last test step of the last test case of a test suite that should be continued by the next test suite of your choice. Essentially you would use this Groovy script as a springboard to jump from one test suite that is just finishing to the next in the sequence. This Groovy script would be used to access the test suite that is next in sequence and invoke
WsdlTestSuite#run(StringToObjectMap, boolean) method on it. Search the forums for hints on how precisely to program this Groovy script.
I hope that helped.
Cheers!
/Nenad Nikolic a.k.a. Shonzilla