How I did it
There are several ways to do this, but here's how I did it and it worked out well for me. (RV6)
I created a form on the fuselage and canopy, from styrofoam, while it was in place and covered everything with clear packing tape, except for the area on the plexiglass and aluminum skirt where I wanted it to adhere. For those places, scuff up the areas with heavy grit sand paper.
Then, drew the outline of what I wanted on the fuselage with a sharpie.
Get some clear plastic and lay it over the whole thing and trace out the size and shape of the piece youwant to make. Cut the plastic and tape it together in order to get a nice smooth template if you have to. You can fold it in half to compare both sides and to make it symmetrical.
Take a larger piece of plastic and lay it over your template on a bench, so you can see the template through it and trace it on to the bigger piece.
Use your first template to cut out the fiberglass cloth, adding about 1/2 inch all around. You can make the skirt in one piece or two pieces, which ever is easier for you to handle. One piece means less sanding later.
Mix up the epoxy (use slow hardener) and spread it on the larger sheet, lay on the cloth and begin saturating it with the epoxy. Do all the layers together at this time, using a brush or credit card to work out all of the bubbles from between the layers.
Once the layers are all saturated, cover the whole thing with another piece of plastic and make sure there aren't any bubbles. Now, you have a plastic sandwich with your glass layer in the middle. Trim away the extra around the edges and carry the whole thing to the plane. Peel off the bottom layer of plastic as you place the lay up on the plane and mold everything to fit the shape. Then you can peel off the top layer of plastic. Then, cover the wet layer with peel ply fabric, which gets pulled off after everything cures, leaving a fairly smooth finish.
Make sure you tape up the plexi and skirts where you don't want the resin to get on it. I used black electrical tape (plastic) at least 2 layers thick for this edge, since you can sand on it with out going through, if you are careful.
how many layers you use is up to you and how heavy the glass fabric is, but for the skirt, I would say at least 6 layers. Others may chime in here. But, you can always add layers on the inside of the skirt, later to make it stronger.
There are a bunch of posts that describe this and similar methods much better, but it is a quick and dirty description. I have used this method to create skirts and intersection fairings and it works well, at least for me.
I'm sure you will get quite a few responses as to how to proceed on this, so I would say pick the one that seems easiest to you.
Good luck.