Read the software package documentation to determine whether certain environmental variables need setting (in .bashrc or .cshrc) and if the .Xdefaults and .Xresources files need customizing.
There may be an applications default file, usually named Xfoo.ad in the original Xfoo distribution. If so, edit the Xfoo.ad file to customize it for your machine, then rename (mv) it Xfoo and install it in the /usr/lib/X11/app-defaults directory, as root. Failure to do this may cause the software to behave strangely or even refuse to run.
Most software packages come with one or more preformatted man pages. As root, copy the Xfoo.man file to the appropriate /usr/man, /usr/local/man, or /usr/X11R6/man directory (man1 - man9), and rename it accordingly. For example, if Xfoo.man ends up in /usr/man/man4, it should be renamed Xfoo.4 (mv Xfoo.man Xfoo.4). By convention, user commands go in man1, games in man6, and administration packages in man8 (see the man docs for more details). Of course, you may deviate from this on your own system, if you like.
A few packages will not install the binaries in the appropriate system directories, that is, they are missing the install option in the Makefile. Should this be the case, you can install the binaries manually by copying the binaries to the appropriate system directory, /usr/bin, /usr/local/bin or /usr/X11R6/bin, as root, of course. Note that /usr/local/bin is the preferred directory for binaries that are not part of the Linux distribution's base install.
Some or all of the above procedures should, in most cases, be handled automatically by a make install, and possibly a make install.man or make install_man. If so, the README or INSTALL doc file will specify this.