Well in linux the programs get separated into library directories and binary directories (like /usr/lib and /usr/bin) anyway. The --prefix option doesn't change the exact installation directory, it just changes the base
install directory. For example if you specify a prefix of /usr/local/myprograms/games then the libraries are still in /usr/local/myprograms/games/lib and the binary is still put in /usr/local/myprograms/games/bin. You can have finer control over this though. Type:
./configure --help | less
(that's the pipe symbol, found next to backspace on a US keyboard) to see what configuration options there are. Sometimes you can specify the exact location you want to install the complete program, but:
1. If you put the binaries in a directory that is not in your path then you will have to type the complete path to load the program, or put a symlink in a directory that IS in your path, or add the directory to your path.
2. If you put libraries in a non-standard location then they won't be in the LD_LIBRARY_PATH so the linker won't find them.
3. Also, if you put libraries in a non-standard location then pkg-config won't find them so configure scripts that use pkg-config to determine what libraries are installed won't find them.
What I usually do (and this is just me, it's not a rule or anything) is I install any libraries that are likely to be used by other programs (things like GTK, Qt, Freetype...) in /usr/lib (by specifying ./configure --prefix=/usr) and any programs (like games, applications...) in /usr/local (the default location for a configure script).