we have been using PVCS from Merant for more than 2 years without much problems.
Since webmethods as such doesnt support any configuration management tool, any 3rd party software you use is bound to have problems one way or other. You will have to be accomodating in nature
Please read Ch 3 "Using Source Control with the Integration Server’ of “Cooperative Development Guide” provided with IS 4.6
This will help you understand limitations of any approach you will follow. (Package level or Component level)