upgrade package to non-slack version
 

I'm running the blackbox window manager (version that came with the slack ware 10.0 CDs). Near as I can tell the latest version is 0.7.1 and the latest "official" slackware package for that is 0.7. So I would like to upgrade to 0.7.1. Seems to me I'd just do the regular non-slack ./configure, make, become root, make install.

Will doing this "over" a slack package cause problems later on?

Before you do that remove the Slackware package first:
I'm guessing that doing ./configure, make, make install will install it to /usr/local, so it wouldn't matter. But to be on the safe side, and to save yourself from potential confusion, you better remove the Slackware package first. Also, you can probably use the SlackBuild script for blackbox to build 0.7.1.