There are many options...
and all have worked.
My thinking was that you will see how the top cowl fits long before you see the bottom cowl. Thus, I fitted the top first and then worked on the bottom.
Just don't forget to take into account engine sag. I did, just not enough.
Before you start fitting them to the airplane, work on getting them to come together around the flange easily first. Once you solve that problem, the fitting the rest is much easier.
Similar to what was described above, I used a
sanding board to smooth the edges. I worked long and hard to get smooth and straight edge on the sides of the top cowl first. The board I had in my hand was 24" long w/ a 120 grit belt 3M 77 glued to it. That worked out well for me, YMMV.
To support the the canopy while fitting, I used
roles of paper towels, which worked great. Once the match drill the top cowling to the firewall, you can return the paper towels to the kitchen.
My bottom cowl had to be trimmed in length and on the sides, so a lot more sanding with the long board was required.