If you are planning on doing a semi trunk chop and use the new shoot as the new leader while also harvesting the old top portion of the trunk to make anew tree then yes, its possible. Not sure exactly what you have planner by mentioning planting it in the same pot, a group multi-trunk maybe?? You can root the desired branch by doingan airlayering with Sphagnum moss (not sphagnum peat moss) if you are planning on the low little branch you would have to cut it off and root it as a cutting but if you are doing just the one its not really worth the time.

The other posts proximity to the window is fine unless it really causes the pot and seedling to heat up badly in the day. That being said as far as germination goes they don't really need any light to do that (just afterward). I cold stratify seeds and in the spring just bring the containers out of the fridge and throw them on top of it, after a week or so the start sprouting on there own. If you are trying to germinate a pine species that grows in a climate with deciduous trees, you may have needed to cold stratify them first in order for them to germinate (unless they where pre-stratified prior to you acquiring them).