How do I keep a customized system up to date?
 

I'm not a Linux noob but now I'm ready to build my own system from ground up and have some theoretical/operational questions. Up 'till now, I've kept it up to date by keeping everything stock and just doing 'apt-get upgrade'. But now...

Programs - How (Best way) do I keep up to date programs to which I've applied patches? Example: installed xfce-panel and applied cairo patch. So, when there is an upgrade to program xfce-panel, do I let it upgrade to new version and apply the patch manually? Or will it upgrade the program and apply the patch to new version? I have several programs with this scenario.

Kernel - How (Best way) to keep custom kernel updated? I compiled a custom kernel with no trouble, including patches. But when I did 'apt-get upgrade' recently, I got the repo kernel with it, which I don't need. How do I keep my custom kernel up-to-date when updates/fixes are introduced to the kernel version I originally used to build mine from? And how do I prevent install of a stock kernel?

Thank you for the info/help.

Recompile from new sources, apt-get or yum or whatever package manager you use won't update custom installed software and if it does touch it in any way it is far more likely to break it than anything else. Same goes for the kernel you custom role you need to recompile to update.

I live by a simple rule, if the repo packages meet my needs I use them. I only compile if I need something in the kernel that isn't all ready available, if a software version in the repo isn't new enough to offer a feature I need (check backports first), or the software doesn't exist in the repos or in a package for my distro (I usually run Debian)

Rolling your own is awesome and great experience, but unless you are using a distro that compiles it's packages like Gentoo or Slackware you will have to compile all on your own for every update you want to apply.