Derrek, thanks for pointing that out, the GUI doesn't really have good support for cladding-pumping yet, I'll add that soon.
Meanwhile you can look at "LaserPerformance.m" line 116 and "AmplifierPerformance.m" line 151 and following to manually adjust your overlap parameters GammaP (for the pump) and GammaS (for the signal).
I have just started using this solver, and I am finding it incredibly useful(update: July 22 2013).
The following comment is with respect to the ytterbium laser option of the program.
It is important in some applications to be able to vary the the cladding-pump/core area ratio. Right now the program appears to pin the E-field/core area ratio to the pump/core area ratio.
It would be nice to include either an input for the pump cladding diameter, or for the overlap ratio so that this can be varied.