Keeping Link Categories Off Index

I have wanted to keep an archive of all of my links, but I don’t want to have certain links on the front page. In other words, I would like to have Category A show 3 links on the front page, but all 115 links in the archive.

I created a LINKS ARCHIVE page using the template, which got me closer but not quite where I wanted. Putting a limit seems to control the number not only on the index but also the archive, which is counter-productive to what I want to do.

Is there a way to limit how many links in a Link Category are shown on the index sidebar, but NOT in the archive? Ditto for possibly having an entire category in the Link Archive but not showing up on the index at all?

You can see my blog at Fairweather Zealot. An example is that I have BestBlogs and BlogRoll. BlogRoll are my favorites, but I would also like to have a rolling list of great sites – but I don’t want 100+ links on my homepage.

Any help would be appreciated. I’m still very new to PHP, so a thorough explanation would help, as well.

Thanks!