Hi Unclejed613,
There is no "base car" -- and there is no "base Linux" either.
Each version of each distribution is really a different system. They can have have components in common, as you would say the wheels or the alternator for cars -- that's it.
And as every distribution is a system - a set of interrelated components, among which a Linux kernel - for it to work care should be taken of the consistency of the system, i.e. check carefully that every interacting components fit together. This (difficult) integration work is IMHO one of the main added value of distribution packagers or maintainers.
Thus in order to keep your Slackware consistent - in other words, not to mess it up - you should take care not to add components (software packages) not intended for it.
So:
1) In order no to miss anything, always do a *full* install of Slackware as proposed by the installer.
2) If you need a piece of software, first check if there is an "official" Slackware package for it.
For instance Java Runtime Environment *is* included in a full install. If you didn't install it initially, it's easy to get afterward, more on that later.
3) If you do not find a software in Slackware, check the website
http://slackbuilds.org. Very often they have a so called SlackBuild for it, which is a script that allows you to build yourself a Slackware package, which will fit with you system and be easily installed/uninstalled with the Slackware's packages tools. They do a very good job quality checking. Instructions on how-to use their SlackBuilds is on their website. It's easy. For instance they *have* SlackBuilds for Adobe Flash Player
4) If you still do not find the software you are looking for, try using a SlackBuild or a package for it on
Robby Workman's or
Alien BOB's repositories. Both are trustful Slackware contributors.
5) If still you can't find the package you are dreaming of, try using an available SlackBuild at
http://slacky.eu. I wouldn't trust them as much as I do for aforementioned people/websites but they do have a lot of packages and are helpful people. Better check their SlackBuilds and use it to make your own package than installing theirs directly though. For instance they do have SlackBuilds for geda. If you use it, remove the line beginnning with "requirebuilder". It tries to do automatic dependency checking but you do not need it and can't run it as you don't have this software.
6) Never use directly a .deb or .rpm package unless you absolutely need it *and* you very well know what you are doing.
To install/upgrade/remove Slackware packages always use the Slackware tools: pkgtool, installpkg, upgradepkg, removepkg and slackpkg. All are installed if you make a full installation of Slackware 12.2 and are very well documented, e.g. try "man slackpkg", it is kind of a Swiss army knife for Slackware packages.