I have two FC7's. How can I get foot controller 1 to use the effects that I assign to it? No matter what parameter is assigned it just does a volume swell. Foot controller 2 uses the super knob as planned
That I'm aware of - all factory Performances except for Multi/GM have the same assignments for FC1 and FC1 (foot controller aka expression pedal plug #1 and foot controller plug #2). They're set as you mentioned - volume and superknob. However, this is something you can change to a different setting for each Performance. You would just need to make a user Performance (your own custom one) and edit these settings.
This runs down how to be sure that the setting is set to superknob. You can trace through the same and change it from "superknob" to something else.
Source: https://www.yamahasynth.com/ask-a-question/super-knob-assign-to-the-foot-controller
4) Parameter Checklist: Press [PERFORMANCE] (HOME). Then press the [EDIT] button. Then user the touchscreen (TS) to select the left-hand menu: "Control" -> "Control Number". Assuming your FC7 is plugged into foot controller port 2 (FC2) - look at "Foot Ctrl 2" and ensure the setting is set to "Super Knob". Whichever port you think should be controlling super knob needs to be set to "Super Knob". If it does not say "Super Knob" then you need to highlight this area and spin the data dial until the box reads "Super Knob".
So, for you, if you do not want "Foot Ctrl 2" to control superknob, you can change the control number from "Super Knob" to some unused number. This would be a CC number. Any unused value will ensure you are not "stepping" on other settings. Once you have assigned the "Foot Ctrl 2" to a previously unused CC value - the superknob will no longer automatically move and you can instead use the expression pedal purely for parameter modulation through the control matrix (control box).
Likewise for "Foot Ctrl 1" you can change this value to an unused one as well. Note that low values of CC are assigned to standard things including CC 11 which is "expression" (a type of volume control).
... and then, this thread walks through (near the middle to end) how to do something similar to what you're asking:
Current Yamaha Synthesizers: Montage Classic 7, Motif XF6, S90XS, MO6, EX5R