I am using 2 inputs for my mic, then I am routing the mics only to output 1…
Then I am applying my Feedback assistant to that output only, then I am using that output and routing it back into input 5 then only sending input 5 to the mains…
As i did not want to apply the feedback assistant to my main output.
The question I have, is this ok? not sure if I am causing any issues elsewhere
Nothing really wrong with doing that. I do something similar with an outboard FX processor - I send it out one of the 6 outputs, into the processor and back into a high-numbered channel which routes to main.
This results in a doubling of the latency (now approx. 1.4 ms), which would certainly only or mainly be a problem if you were using this signal to feed your own in-ear monitoring, or if you intended to mix these two microphone channels together.