Oh, I faced this problem so often :)

I would recommend you creating one directory, call it eg. "project". In 
this directory you create a subdirectory "universal" with files that are 
independent from the controller type. In that "universal" directory you 
have one entry file, for example "universal.c" which includes all 
necessary headers and files.

Then, create a second subdirectory in the "project" directory, call it 
eg. "ATMega8". In this directory you create a project that uses the 
specific controller (in this case ATMega8). In the "main.c" you #include 
the "universal.c". For this, you have to add the directory path 
"..\..\universal" in the compiler settings.

Like this, you can create multiple other subdirectories in the "project" 
folder for other controller types and you don't have to create redundand 
code.

I hope I explained it understandable :)