Hi Eddie,
I did my front windowns last autumn. When re-assembling, I used the 'ribbon' type mastic from a roll and I applied this around the window aperture - mainly in the recess but a small amount folded over the outside edge of the front panel. Next, I carefully placed the clean seal over the mastic, ensuring all of the screw holes lined up and then firmly pushed into place, especially in the corners. I used a piece of old broom shank to 'roll' over the seal to flatten down like a rolling pin. Once pushed fully into place the 2 ends of the seal should meet and touch with no surplus. I then stapled the seal into position with a staple gun, firing through into the frame. Finally the capping strip was re-inserted, the hinges and stays re-fitted and all adjusted to ensure a good all round seal between the window itself and the rubber seal.
I'm not saying that this is the only way or the correct way to do this job but it's the way I did it based on some information that I had read. Hope it helps?
Good Luck!
Simon