As my wife would say "stupid semantics", she's an English teacher.  

Ok, I see.  IMO I wouldn't pot the rooted cuttings up until I see significant roots, branching roots, and some top growth, I would leave them in the perlite cups until that time.

Then I would "pot them up" ( I usually go to gallon containers from cup phase) into a potting mixture of at least 1/2 perlite (from said cup).  Like Hoosierbanana suggested Pro Mix BX is highly rated for it's consistency of giving good results.  Lots of others have their favorite soil mix, for example I use pine bark fines, very cheap and readily available here, but you'll get lots of different answers as to which mix is preferred.

Whatever you do make sure the mix drains well.  Personally, I would rather water more often with a porous mix than water less and take a chance with rot.  

People are going to get mad at me, but I start with perlite cups, I skip the whole place in baggie/whatever method.  I do have losses, but most of the time it's after the pot up stage.  Just be sure to be gentle with the roots, they will stick to the sides of the cups, and gently place media around the roots.

I'm currently trialing a even simplier method (I don't have results yet so try at your own risk).  Into 1/2 gallon Root pouch add Pro-Mix + Perlite wet, add cutting, place on heat pad, don't let completely dry out, wait.  That's it.  That way I'll avoid pot up death since roots won't be disturbed.

Good Luck

One can grow in perlite, often greenhouse tomatoes are grown this way....but they are watered (fertigated) several times a day.  It's hydroponics in a nut shell.

Your right, I haven't seen any fungus gnats with perlite.  I personally like it, but as I mentioned it's the pot up from cups to gallons where I would experience problems, so I'm trying to figure out how to avoid the cup to gallons pot up to begin with.

This year, for the first time, I am rooting cuttings in water, just to try it out.  I am anxious to see how it goes.