Hiya jlagana2002,
Here's an attempt to explain my understanding of it (anyone else jump in if I am off course)
1) The tone stack in an amplifier is (as far as I understand) the circuit that handles the Bass, Middle and Treble controls. Each tonestack is different. For example the Bass control on a Fender Twin might boost a different frequency to say the bass control on a Mesa Recto. Same goes for the treble and mids. Lets stick with this example and mention that the bass control on a Mesa (now I'm not saying this is the case - I don't actually know), might be able to boost the bass frequency further than a Fender can, at the same time, the boost on the Mesa may only apply to a narrow band of EQ, while the Fender might boost over a broader range of bass frequencies. So this goes for each amp. Certain amps don't even have mid-range controls, and so they have their mid-range set to a particular value. The other thing to consider is some tonestacks may be more interactive than others. For example boosting the bass on one tonestack might mean you can get more highs out of the treble control, when its boosted. Each amp is different. Also important is the placement of the tonestack in the circuit. Some amps place them before the preamp (ie before distortion), while others place them after the preamp, but before the power amp. The Axe-FX gives you the capability to even place it after the power-amp for even more tone-shaping options. I look at it like being able to hack the Bass, middle and treble from one amp, and slap it into another amp for interesting tonal effect. You could make a Recto sound more vintage by putting an old marshall plexi tonestack into it. Remember there are implications for overdrive too here as some tonestacks might be able to overdrive a particular amp in a different way to their stock tonestack.
2) The crossover block in the Ultra splits the high frequencies and the low frequencies and is able to send them to different places. For example, you might want to keep your bass tone cleaner, while adding more overdrive to your upper frequencies after your signal has gone through the crossover. Its like the sub in your home theatre. A lot of them have a crossover so they only handle the low frequencies, thus assisting in the clarity of the music produced as they don't have to scramble to reproduce the high frequencies (which vibrate the speaker differently to low sounds) at the same time.
I hope that helps. Best advice, use your ears. As I heard a wise man here say, "if it sounds good, it is good". Happy tonestack swapping!
TimmyM
