I have been reading a good number of articles about how to keep your software up to date on your computer (portupgrade) but can't find someone explain one thing I can't understand. So I install some large software using ports, say Gnome as it takes me about 2-3 days to compile it on my computer, so naturally I would install this with a package. But eventually, new versions of the software comes out (or since I installed it from a package, there may be a newer port already out) and portupgrade will try to install this new version using ports (assuming a package hasn't been released yet) when I run the -a command to keep everything up to date and begin the 2 day process. I don't know how to avoid this problem unless I specifically use caution to portupgrade every individual piece of software instead of using -a until a package release comes out. Is there a better approach to this?
Another thing: it would seem to me like every time I want to upgrade something I should use -rR commands with portupgrade to keep everything consistent, but I often find articles being very inconsistent with using -rR or just -r or -R or nothing at all. Is it typical to always use -rR and why not if you dont?