Jim likes to say that the only stupid question is the question not asked
As far as the set up of those URL's, if I'm even in the slightest of bad moods, I tend to just decline the submits with all kinds of numbers in them (unless it's the date) There's too many things that you can do with URL's & directories that will benefit you & numbers, IMHO, are not one of them.
I assume that you want to use one of these little assistance programs because it does the recips for you - while it might be a pain in the ass at 1st, once you get a system down with what linklist has what categories, it's really not that hard to go to a bookmark, grab the recip & throw it on the page. (assuming that it's a niche/category specific recip - otherwise, just start a page on your hard drive with the sites that have general recips & just copy & paste them as needed)
Most of this stuff is a big pain in the ass when you 1st start - but as time goes by you'll set up a system to cut down on the time it takes to do these things & life will be easier