Just reverse the sweep values in your controller settings for your wah by flipping the 0 and 100% values at "start" and "end", that way you reverse the sweep of your controller.
If you don't know what I mean, just watch this video blog from Chris as he shows how to change sweeps in the controller settings and more
Mission SP-1 Pedal with Fractal Audio Axe-FX II and MFC-101 – How-To/Tutorial – 3 different uses : Katsu Kuri Media Blog
That's why I'd advice you to adhere to the KISS principle at least in round 1.
Perhaps base your first presets around the same template, so you always know what you have and where it is in your signal chain.
I took some screen shots of a basic template but for some reason I can't get them to upload to this post.
You could make a grid like this:
input - wah - comp - parametric eq 1 - amp 1 (tube pre amp) - graphic eq or the efx loop block with your own external eq inserted - trem - parametric eq 2 (for mid boost) - filter 1 (for volume boost, null filter and up the gain db) - split the signal i 3 rows for paralleled chorus, reverb and delay - perhaps sum the 3 rows back to one and insert a multi band compressor if you are used to using one, otherwise just parallel the 3 rows to output - output
Experiment with the tube pre amp sim vs just an eq and see what you like best with your guitars and for the sounds you are going for.