EPC installs a new set of basic libraries regardless of whether the tick box in custom install is checked or not. Backup your custom libraries before installing!
I would recommend that you move the library from the default Easy-PC location to one of your own. Mine is in a separate directory that I version control using CVS. That way you won't get stung by an install overwriting your library (by not ticking the box or a erroneous installer package).
TIP : I also don't use the supplied library due to the number of errors (i.e. SOT-23 pin numbering) that has caused me to put quite a few big surface mount prototypes straight in the dustbin !!
I've built up my own database over time validating every component before using it in a project.
A good solid library is key to any PCB CAD package :-)