This is another 'I get asked this all the time' post so hopefully what follows will help.
There are two basic products we recommend for re-bedding windows; GZ tape and bedding compound (in a tube). Both are butyl based. The tube product has the potential to be very messy (think stringy cheese in a 1980's fondue party), but works very well. A common issue however is that by over tightening when refitting, too much 'goo' gets squeezed out leaving little to seal your frame to the boat. Ideally, I'd like to see 1mm of bedding product between the frame and boat at the end, as this will allow for an effective seal which can accommodate slight movements as your boat twists and turns in rough weather...
GZ tape comes in a 12m roll and is nominally 10 x 3mm rectangular section. When fully compressed the depth reduces to ~1mm but no less. Hence we achieve our 1mm gap. We stock GZ tape in WHITE and BLACK, though most specify/use WHITE
If you have a wider flange (the part of the frame which presses against the hull) you can use a combination of GZ tape and 'goo', utilising the GZ tape to enforce the 1mm gap. If your flange is narrow (~12mm as common on Lewmar ports) and bolted through then we suggest just GZ tape. If the frame is screwed, not through bolted, then stick with 'goo' as the force required to compress the tape may exceed what screws alone can achieve. In such a case you can use small pieces of 1mm chocking rubber (or similar) as spacers placed on the flange to enforce the 1mm gap. If so, dry fit the window first to identify any 'hot-spots' on the GRP so that you can ensure spacers are placed in these positions.
Note that some frame flanges are not flat, but have grooves or channels on the underside to trap bedding compound, even when tight to the boat. If yours are such then you may not need the 1mm gap as these channels may be providing a buffer already. My personal view is that having a 1mm gap in all cases just avoids any potential issues and is likely to result in a longer lasting seal.
Before refitting starts, clean the flange and GRP with a suitable oil-free solvent such as IPA, Acetone or Methylated Spirit. Not White Spirit as this will leave an oily residue. If painted, be careful using Acetone as this can be quite aggressive (as on some plastics too).
Applying GZ
So, if using GZ alone, you're set. Just place the tape around the flange, then cut and join the ends. Whether you have the join above or below is personal preference but should not make any difference as long as the tape ends are butted together.
If the fasteners pass through the flange then use a spike to form the holes in the tape. Do not use a twist drill as you'll just end up with loads of tape around the bit ie a mess. If fitting Lewmar ports the fasteners are inboard of the flange so no problem. In both cases fit the window and bolt up a little at a time all round until you have the 1mm gap. You're done.
GZ with 'goo'
If using GZ and 'goo' then you need to decide whether to put the tape on the inner side of the flange (ie closest to the channel holding the pane) or outer. This is what I suggest; if the frame is a tight fit in your cut out (the hole in your boat), put the tape on the inner side and the 'goo' on the outer. This way any excess 'goo' will squeeze out around the outer edge of the frame/flange. If there are gaps between the frame and cut out then you can consider putting the tape on the outer side and the 'goo' between the tape and the channel holding the pane. In this scenario the excess 'goo' will squeeze into the cut out gap, potentially increasing the sealing. Either can work, but note that the 'goo' and tape are laid side by side and not overlapping (or worse one on top of the other). As mentioned above, if the fasteners end up passing through the tape make the holes with a spike. If using interscrews, using fasteners through tape may well help prevent pushing 'goo' into the captive bush (the closed ended nut part). 'Goo' in the bush has no where to go so may prevent full tightening or reduce the range when screwing in.
For more, take a look at my previous post about refitting the Canpa hatch to my boat as this shows using GZ tape and 'goo' together and includes details of preparation and clean up.
I'll update this later to include photos but for now the above should guide you sufficiently.