Merging is a functionality provided by a source control system - you can use Git. You will need some sort of client to be able to perform all the source control functions, only one of which is merging differences. Eclipse has a plugin for Git, so you should be able to use that.
The SoapUI plugin for Eclipse gives you only SoapUI functionality.
Have a discussion with someone from your development team about merging code and resolving conflicts in _any_ code. SoapUI is irrelevant to this problem, and will not help you in any way!
