If this has been discussed before , sorry for re posting , but I couldn't find anything through the search function so....
I am wondering if there is a difference if the drag is on a horizontal surface say like a wing , opposed to a verticle surface like the side of the fuse...excluding argument of the surface area of the two examples I have mentioned.

I want to make a cowl that encloses my engine and pipe.. and want to know if there is a difference if I just make the cowl a flat surface over the top of the engine and pipe or mold it to more of a knife edge

Here is what one of the top contenders in last years German Speed Cup did.

Smooth, rounded and minimal like shown in the pic is best if speed is the goal. For sport flying it won't make any difference that you'll notice. For an aerobatic model that'll be doing knife edge the sharp V would allow for more side area.