I am currently using checkinstall to install quite a few software not present either in official or in Linuxpackages.

I am using swaret to keep the system up-to-date using swaret --upgrade and to install packages found in the official repository.

Will this create a conflict later on or is it safe to combine these methods

I think it is perfectly safe to combine these methods. The only time I've ever run into trouble is if I recompile an official Slackware package, like the beta for wireless tools or recompiling visudo so it can use pico instead of vi. When I do this, slackpkg tends to think that these are older packages than what is available and will revert to the official Slackware package if I let it. Swaret might do the same thing. However, I've never had any problem with checkinstall packages of things that are not part of the official Slackware repository. However, I also don't keep synced with Linuxpackages so that may introduce a new wrinkle or two.

In general, I think as long as you are paying attention to what swaret is doing, you should be fine.

I haven't set swaret to point to linuxpackages. Just the official Slackware-current. Also I just tend to download and install packages from linuxpackages or compile otherwise. Is that ok?

yes. That's good.

Does swaret have a blacklist file like slackpkg? I tend to blacklist packages that I've built myself for that very reason.

It has an Exclude list in /etc/swaret.conf if that's what you mean.

I've never had an issue with Swaret/Checkinstall

No problems here either. My system is probably half packages I compiled and built, and the other half from the official Slackware trees and Linuxpackages.net.

Checkinstall will actually make upgrades go a little more smoothly, because you can then avoid conflicts by uninstalling programs more cleanly.