I have a bunch of primaries and secondaries. Just wondering is there going to be any difference in arrow flight between the two?

Yes primary are stiffer and hold up better
Secondary I use for stumping

Secondary may be noisier too

There won't be any difference in performance if your arrows are tuned properly. As said above they won't be as durable but will still last as long as a new stock commercial feather. They can be a little noisier but shape has more to do with that than the type of feather. Personally I'd prefer a secondary feather over a commercial feather any day.