To answer your first question, yes.
[pause for laughter]
Which is to say, the model computes fluxes for the given energy and greater, so if you specify some low energy E1 and some high energy E2 in a single run, the flux values you get back for each energy is for that energy and greater. So yes, the flux for the energy range (E1,E2) is found by the subtraction you derived.
The B-L coordinates system makes grown men either cry, drink, or both. And for any practical purpose, no one uses the web interface or computes the McIlwain coordinates by hand. In fact, I'm pretty sure I would have to spend a morning with McIlwain's paper again before I could even remember how to do it. The practical way is to use additional computer programs from NSSDC at Goddard that automate converting from geodetic coordinates or orbital elements to B-L coordinates, and further automate stuffing long sequences of B-L coordinates into the AX8 models, which they embed.
I think Jim Vette wrote most of that code. NASA/Goddard repackages their software approximately every eight minutes, so I don't know off the top of my head what package it's in these days, or if you have to pay for it. Let me check.