"for example i want to upgrade the Nautilus window manager in Suse. I want to replace it with the source version of the program. How would i go about installing Nautilus, in a way where i dont have duplicate copies of Nautilus installed on my system.????"
The best way to keep things straight when you do your own compiles on a rpm based distribution is to first compile your source into a rpm package and then update the rpm package in the normal way. The key to creating your own rpm is to use checkinstall.
When you use checkinstall as part of a compile the command sequence for the compile becomes:
Then you use the resulting rpm package to upgrade or install the package in the usual manner using rpm.