One:
The window seal comes in one piece. It is intended to get a razor knife cut in the corner to ensure a good fit. Bend the seal around the corner with as tight a radius as possible, then cut it. It should then fit tightly into the corner.

Two:
The more likely issue is that the window needs adjustment. This can be a frustrating task but is do-able. The procedure is too complicated to outline here but can be found in any version of the CD-based repair manual. If this is the problem, try the adjustments accessible from the outside of the door frame first before removing the inner door card. These adjustments affect the window in-out tilt and should fix the problem in most cases.
As a quirk, the instruction says that the window adjustments be made to the soft top, then the hardtop itself be adjusted to fit.

Good luck and keep us posted.