If and how this works heavily depends on how the plugins are written, so before going into this trouble you might wanna check what's actually causing the interference. In any case, this is potencially a lot of work and it might not work at all. But there is no easy answer on "how do I do it?", so if you're not too experienced, this is not really an option for you, sorry.
Did you try changing the order you load the scripts in?