I'll try to provide some basic advice and usage hints, on one condition.
When you reply, DO NOT mention your Fender Mustang unless it's to say "I sold the Catalyst and kept the Mustang".
I really don't care and don't want to hear it.
So, my first piece of advice is to sell the Catalyst and keep the Mustang. You seem to like it a lot, why not go with what you know?
If you want to keep the Cat, and you bought it at a store with a proper return policy, take it back and swap it for a Cat100. You'll see why below.
Assuming you've decided to keep the Cat, here goes:
Start on Bank 1, Channel A. See Page 8 of the Pilot's Guide. DL it if you don't have the hard copy.
Once you've done that, start by pressing the MANUAL button. Use the Amp Selector Knob to select an amp. Turn GAIN OFF (full counterclockwise).
Turn all of the Tone knobs to noon EXCEPT Presence. Turn Presence OFF for now. Effects and Reverb OFF.
Set Wattage at .5 watts, Channel and Master at noon. While strumming, slowly turn up the gain to a pleasing level.
Starting with BASS, while strumming sweep each tone knob end to end and back, noting what they do and stopping when it sounds nice. The tone knobs are somewhat interactive, so note also how they interact. Certain tone changes, especially around the midrange, can affect the GAIN, so keep that in mind as another potential interaction.
When the amp sounds nice, press and hold the Channel A button until the LEDs start blinking.
Now press and hold the Channel B button until the LEDs start blinking.
Switch to Bank 2 Channel A. Repeat the above process with a different amp.
When you reach Bank 6 you'll have 6 2-channel amps, each with both channels set identically.
Now, grab a beverage, sit down in your recliner and READ THE PILOT'S GUIDE! Pay special attention to the Catalyst edit section.
While you can select FX/Reverbs from the panel, you can't set their parameters from there. The whole process of dealing with the FX/Reverbs is SO much easier from the Edit Screen. Overwhelming? IT'S ONE SCREEN with a couple of dropdowns!
As to the footswitch and two FX limitation. This is not a modeling amp in the same way as the Mustang, L6 Spider or Peavey Vyper.
Your two button FS controls the Channel and either the FX ON/OFF or BOOST ON/OFF. If you use it for BOOST you can set the B Channel to have the FX ON, and thus mimic an FX ON/OFF Switch. ITRW, the second channel of a two channel amp is usually the LEAD CHANNEL. Think of it that way. Also, if you MUST have more FX available at all times, you can put OD/DIST/FUZZ pedals between the guitar and amp, and you can put Mods/Delays/Reverbs either before or after the amp in the FX Loop.
NOTE: The FX Loop is NOT between the pre and power sections in the same way as a traditional amp. The power amp of the catalyst is more like taking a line to a PA. FX placed in the Cat's FX loop function more like Rack FX in a studio. While I'm sure that somebody has done it, it's rare that someone would put a FUZZ in a Rack in the studio!
Keep in mind that you don't HAVE to use all 6 amps. You might only use a CLEAN, a CRUNCH and a HIGH GAIN amp, but use two or 3 Banks for each, with different settings and FX in each Bank. Once you've become familiar with the amps through the above suggested procedures you'll be able to narrow it down to your favorites. For instance, I mostly use the Boutique, Crunch and Dynamic amps.
Which brings us to the question of switching Banks. You either do it manually from the panel (not practical in performance), or you get a MIDI FS. The MIDI knowledge required here is neither VooDoo nor Rocket Science, but MIDI switchers are an extra expense. It doesn't sound like you're ready to jump into a gigging band just yet, so worry about it later. For now just consider what I said above about swapping your Cat60 for a Cat100. You can't just plug a MIDI controller into the Cat60 without being tethered to a computer like you can with the Cat100, and the external host box required to use MIDI with the Cat 60 away from a computer costs about the same as the upcharge to a Cat100.
Earlier in this thread I posted a couple of summaries of what's NOT in the Pilot's Guide. You can also find a lot of info here:
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Posted by Elantric, who also posts in the Digital and Modeling Forum on The Gear Page.
I've given you a lot of homework to do. Do it and you'll be happy with your Catalyst. Or not. But at least you'll know why, and you'll have learned a lot in the process.