I usually drill in a corner to get the piece anchored. Then drill and cleco every other hole. Then come back and drill the inbetweeners.
I also don't have many cleco's, maybe 20 1/8".
No right or wrong way to do it really.
Before you take your panels off the car mark the back side around the frame members with a sharpie. This way you have the template to measure and make your rivet holes. Drill the aluminum, deburr, and then put it back in the car to drill into the frame through the aluminum holes you already drilled.

HTH,

John