I've not heard of Webtrends being used with RH, although someone out there might be. If it helps others use Google Analytics and I have found the following posts that cover how to do this:
The second link covers how to add the code to a master page which would address your second concern.
I tried using both of those posts as a starting point. Some of the information would seem to be similar, but those posts are very old, and mention using some features RH 7 and RH 8 (template pages). I find it very surprising that there isn't more information on this subject, if not for Webtrends, at least in general. It seems as if Adobe might like the answer to lie in the purchase of RH Server...
Although templates are now Master pages, it works the same. Old, but WebHelp still has the same buildup. So you can use the same method: put it in the master page, or use a find and replace operation to add the code post generation.
Obviously Adobe have a vested interest in getting people to use RoboHelp Server but as others have said it is not strictly necessary. RoboHelp Server does have some distinct advantages over other analytics applications but you can get by with third party solutions.