Here is how I do it...
1. Create the directory $HOME/MySystem
2. Add the following to my $HOME/.bashrc
Code:
if[ -d $HOME/MySystem ]; then
PATH="$HOME/MySystem/bin:$HOME/MySystem/usr/bin:$PATH"
export PATH
fi
3. When building software, pass --prefix=$HOME/MySystem/usr to the configure script.
Step 2 ensures the version in $HOME/MySystem will be found before the system-wide version. Step 3 will need to be modified as necessary depending on whether the package uses autotools, cmake, etc.
This is also how I manage Python and Perl modules. When I use easy_install or pip to install Python modules/packages they go to $HOME/MySystem/usr/lib64/python2.7/. Similarly for using CPAN to install Perl modules.