Fit the rubber seal to the body opening, not the other way around. If there is a seam on the rubber where it's bonded together, I've always seen these put at the bottom. If the seal you're installing is a linear strip that you cut to length... fit it to the body pushing it securely in place as you go (no slop at the corners and no tension on the rubber) and cut it at least 10mm too long. Put adhesive on the cut ends and place them together as you re-adjust the rubber in the window opening. You want this long and pushed out to the max opening of the body so when it shrinks over time it won't pull apart. Let the glue dry if applicable.
Once the glue joint is set, place the bottom edge of the glass in the rubber seal. Use a nylon spatula (or putty knife from the DIY center) to lever the rubber over the top of the glass as you push it down into the rubber seal. Do not use a metal tool and do not use a screwdriver. (You'll cut the rubber, your paint, or your hand if you use a metal tool).
To install the locking strip you need the special tool. There are a couple of types and you can make your own. Do a Google search and I'm sure you'll find details on the tool.

Decision Time: What condition is the car body in under the seal? If it is rough or otherwise in question you MAY want to consider working some windshield sealant or clear RTV silicone rubber between the seal and body and the seal and the glass. It's up to you. If the car and rubber are in good order you shouldn't need the sealant. However, sealant isn't a bad idea EXCEPT, it will make getting the glass out later a more difficult and messy job. It's your decision. If you put the sealant on now, the excess will be squeezed out when you insert the locking strip. Be sure to wipe off the excess before it cures. I prefer very soft, clear, flowable RTV to the black goo some glass shops use.

To insert the locking strip, moisten it and the rubber seal with a little dishwashing soap. Starting at the bottom, insert the tool and locking strip into the sealing rubber. Draw the tool up and around the seal as you push the locking strip down into the rubber. With the tool this goes reasonably fast. Try not to put any tension on the lock strip. If possible, PUSH it into the seal from behind so there is no tension on it. When you've gone all the way around, cut the locking strip a little long... perhaps 3 or 4mm. Then force the cut end of the strip into the seal and cover with the trim piece if you're fitting one.
The locking strips will shrink more than the rubber so you really want to make sure you aren't putting any tension on this when you feed it in and you want it cut a little long to allow for shrinkage.

The first time you do this it's a learning curve and it might take you a little time and effort. The next time it will go very quickly. Treat yourself to something nice with the £120 you saved.