Not sure from your question what it is you are attempting to do. Do you have the same application stored in two different places on your HD and want to have an applescript access/use/launch only one of the two? If so, use the path to the desired app when referring to it in your script.
There is applescript code ' using terms from' that keeps the focus on one app when there may be different versions of this app installed. If this is relevant to your situation and you want more info, be glad to try to help.
Craig