Addon domains and robots.txt

I need some clarification if anyone happens to know this:

OK on my hosting account I have 3 addon domains. My main site for the account is on my hosting server under /public_html/. The three addon domains are in subdirectories of the public_html folder , public_html/addon1/, public_html/addon2/, public_html/addon3/. Well I have a script on some of the pages in my main site that lets you search my site as well as a dynamic php sitemap. The problem is that sometimes these search within the subdirectories that the addon domains are in and have somehow caused a few of those pages to be indexed under my main site. (ie: Google shows results for http://www.mainwebsite.com/addon1/addon1index.html)

So I figured I could add a robots.txt file under my main domain (in the public_html folder) and disallow addon1 addon2 addon3. Will this cause any problems with getting my addon domains indexed under their correct domain names? It doesn't seem like they would, but I want to be sure. Should I include a robots.txt in all of their folders that doesnt disallow anything? I only ask because I added the robots.txt about 2 weeks ago and suddenly dropped off yahoo... not sure if this is why though.
thanks