I've tried parallel clamps (as shown in the manuals and videos), Bessey clamps, and most recently, with a jig fixture clamp in the T-slots. The Kreg pocketscrew vise-grip like clamp works well enough for me, but the wife has difficulty clamping with enough tension. It's always hit or miss, taking several attempts before it sits square, straight, and flush. Surely, not everyone has this problem.
I lock the fixture to the fence (such as that were) with the middle screw, and weight down the back of the fixture with a jar of coins to balance out the clamp's weight. The t-slot clamp would almost work, but tends to pull the board a little as it snaps over into the lock position. The Bessey and parallel clamps seem to need more hands than the two I have.
The fence is square upright to the table. The right angle fixture is square to the fence and table. The router insert is flush with the table, and not free to move. The stock is square, straight, and flat.
As critical as this operation is to even passable joints, I find the right angle fixture extremely difficult to get right. I've tried everything I can think of, short of just holding the boards by hand. (Does that work?) Maybe it would help if you would talk me through your procedures and setup. Joann, my wife, is new to woodworking, and frustrated now close to giving up. (She wants to build a table while we figure things out. Go figure.)