I have been using stow for couples year (still a very junior user) and it is very good software management tool. But I come across module about 1 year ago and found it is even better ( will discuss it in other post.
To use module, suppose the module was installed under /usr/share/modules
1.source the module init file
. /usr/share/modules/init/bash [if you are using csh or other sh, choose the right one rather than bash]
2. use the right module files
module use /pkg/modulefiles
3. module load a module
module load R/3.2.3
4. remove a loaded module
module rm R/3.2.3
5. remove all loaded modules
module purge