Section 508 Search ability

I'm brand new to RoboHelp (v6), so forgive the elementary question. The "Search" function for Section 508 compliance appears to be limited, to put it nicely. The results appear to be similar to an Index, only much less helpful, returning words like "above" and pages upon pages of other unhelpful words we used in our topics like "system". I understand the need to create a Stop List for these terms for the Index. However, before getting in too deep with RoboHelp I was hoping someone could validate that entering terms in the Stop List for the Smart Index will remove the terms from being picked up in the Search function? For some reason the documentation doesn't make that clear and I'm unable to test it because of a separate issue posted to the forum. Also, because Section 508 is the requirement and a non-508 webhelp is not desired for any other reason than to implement a search using a text field (for non-508 users, of course), is it less of a maintenance hassle in the long run to implement a third-party tool like ZoomSearch, or is a non-508 webhelp option better?