I just got my new pop-up blind from Eastman Outfitters.
The shoot through screenwindow is not vey big, I dont seemyself using that.I guess I would just use the open window with no screen. My question, if I just use the open window, will the deer see me in the blind? Is it effective having the open window? I only plan on having the window open enough to shoot out of.

If the light is right, a deer will be able to see you inside. For instance, if the sun is shining into your blind from behind the deer, they can see in. BUT if the deer is looking toward the sun and the sun is behind you and the blind, it will look black inside, and they won't be able to see you!
It's a good idea to wear black, or at least dark clothing while hunting from inside a blind, that will help in keeping you hidden! Also, keep your movements slow jsut in case!

Ditto on the black.Also if possible set upso you dont have to open the window behind you,so they dont profile you

I've found that the deer really zero in on the "black holes" created by the window openings so shoot-thru mesh is MUCH better! You can buy the shoot-thru mesh and configure it over ANY and ALL windows you want. IMO, this would be the best choice.

Throw a ditto onto what Cornfed posted. If at all possible I would stick with the mesh. Have you at least tried to shoot out of it? If I cannot convince you otherwise then definitely follow through on wearing the black and not silhouetting yourself.