Yes - it's a little tricky.
Does there need to be any cutouts made in the cowl for such things as cylinders? - if so then this is what I do.

I make a "dummy engine" - this consists of a flat ply plate with small holes (about 1/16" - just enough to get a pencil through them) in the correct location for the engine mounting holes. - in the crankshaft location (usually in the centre of the hole pattern but not always) I glue a large piece of round wood (a cut off piece of broom handle works well). That wood is longer than the engine itself but it usually has a mark on it at the length of the engine (from the back of the mounting holeds to the prop hub). I also make a cone that fits fairly neatly over the "centre pole".

From there it is easy - Put the dummy engine on the firewall, Install the cowl in the preferred position, place the cone over the dowell so that the dowell is centred iin the outlet of the cowl (I got that idea from an automotive clutch aligning tool), roll the plate around so that the holes are horizontally/verticall aligned on the firewall and use a pencil to mark the bolt hole positions (or you can just have the centre line positions marked on the plate of the tool).

You can then also remove the cone and use a rule to measure from the front of the cowl to the mark where the engine length is made and there (plus a few mm) you have the dimension of any standoffs you might need.

Unfortunately, I am not near my shop at the moment or I would photograph one - I hope the description above makes sense.