No, I don't think there is a way around that problem.
Even if you were adding a hack manually, and it asked you to search for X text, and replace it with Y.. You'd have a hard time if your board was hacked up completely.
I think that if you have a hack installed the affects one area of code, and then try to install another hack that affects the same area of code, they may essentially have similar features. That being the case, I'd reccomend that you choose between them.
Hope I helped.
------------------
Author of Script Hack Wizard
http://www.scripthack.barrysworld.net