One second. What do you mean you connected your guitar through it? Traditionally, you'd connect your guitar straight into the Axe III. The EV's are typically used as expression pedals. The FC-12 and jacks do not carry any audio at all. You can't send audio over FasLink.
But yes, you can use the EV-1 for Wah/Volume as desired. Usually, you'd do this inside the preset, so you'll need to remove any global output or global input configurations you have.
One possible setup would look like this:
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