That's what I normally do. It works better if you use darker pieces on top of lighter, although Monokote white is pretty opaque. First I cover with the light color, and shrink normally. Clean the surface really well, because little bits of dust will show through (if you care).

Then cut out the smaller pieces. Spray the surface lightly with Windex. Lay the pieces where you want them, and, using an old credit card (or similar), squeegee out all the Windex. Some people like to cover the credit card with a paper towel to prevent scratches, but I'm not that fanatic. Make sure you wipe the pieces until no water comes out the edges.

Let dry over night at least. Now you have two choices. You can go over the edges lightly with a not-too-hot iron, or you can take a Q tip, dip it in Monokote solvent, and run it around the edges. I like the solvent method, but some Monokote colors bleed pretty badly, which is a huge pain. If you use solvent, make sure you have good ventilation in your work area, or you'll be flying (you, not the plane) after 1/2 hour (or have a huge headache).

There are people who swear the Windex activates the Monokote glue and you don't have to iron down the pieces or use solvent. That's not been my experience, and I've run quite a few tests.

For smaller pieces, I use a two-step method and trim solvent, to avoid the Windex step. I hold down (or tape with masking tape) half the piece. I lift up the free half, and apply trim solvent to the base covering. Then, starting at the mid-point, I smoothly press the trim piece down, wiping sideways to avoid bubbles. Now 1/2 is attached (you only get one chance with trim solvent!). Now I pick up the other half, and do the same thing.

By the way, the same process works for the adhesive type trim sheets, and for small designs, they might be a little more convenient. In that case, once the Windex completely dries, the adhesive takes over and you're done. In my experience, the self-adhesive stuff is a bit less reliable. In other words, after a season of flying, you're much more likely to have a corner lift up with the self-adhesive stuff.