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It's entirely possible to install both Fuerte and Groovy side-by-side. The typical configuration is to run using either release (not both), to avoid conflicts. It may be possible to try and mix packages from fuerte and groovy releases, but I bet you run into compatibility issues. Other than that restriction, there aren't really any cons to this setup.

Binary Packages

The debian binary packages will install to different locations:

/opt/ros/fuerte/...
/opt/ros/groovy/...

If you followed the Installation instructions, you will have added a line to your ~/.bashrc file that references the setup.bash file in one of those installation locations. To switch to a different ROS release, simply reference the setup file in the desired distribution directory. The Install instructions refer to this in section 1.5 ("Environment Setup").

For a "temporary" change (affects the current shell only):

source /opt/ros/groovy/setup.bash  (or fuerte)

For a "permanent" change (affects any new terminal shells):

1. change the line in your ~/.bashrc to reference the desired ROS setup.bash file
2. run source ~/.bashrc in any open terminals (or close and re-open)

Source Packages

If you're using installing ROS from source (or using supplemental packages from source), you'll need to use a similar approach. In this case, the easiest method is to install all fuerte packages under one common directory (e.g ~/ros/fuerte) and all groovy packages under a different directory (e.g. ~/ros/groovy).

Then, you switch between releases by adding the appropriate subdirectory to your $ROS_PACKAGE_PATH:

export ROS_PACKAGE_PATH=~/ros/fuerte:$ROS_PACKAGE_PATH

NOTE: many packages work equally well with either fuerte or groovy ROS distributions. For these packages, it is not necessary to maintain separate "fuerte" and "groovy" directories. Check with the package maintainer to see if there are any issues you should be aware of. Or just try it and see if it works!