General :: Install All Files Of Package When Compiling?

Where is the best path to install all files of package when compiling?

For example - I want to install ProFTPd, so there's an option

--prefix=/usr/local/proftpd

, which means, that all files after compilation (including binary and configuration files) will be stored here. As you know, all packages, which are installed via package system (like zypper on SuSE or apt on Ubuntu) usually stores its configuration files in /etc/ and binary files in /sbin/ and also stores a link in my $PATH, so i can run in just by typing proftpd (without /sbin).

The huge advantage of packages installed via package system, i think, is easy uninstall process. I'd like to be able to uninstall compiled packages also easy.

I think i could be able to create some batch file, which I'll be able to use like this:

uninstall --package=proftpd

And my script will find all proftpd files in usuall paths (/etc, /sbin) and remove it using rm.

Is there any best practices, where to store all these files, or are there any (dis)advantages of my first example (--prefix=/usr/local/proftpd)?

I really don't think, that it's nice to have 2 paths with configuration files and binary files, but maybe I'm misunderstanding the basic principals of Linux... :-)