How can I trust a local window manufacturer? What to research or check?
I guess it depends what you mean by quality.  It seems like the only thing you are interested in is the frame.  You have no requirements around the glass?  

I've bought windows from a small manufacturer before - they forgot to drill the weep holes.  Post drilling the weep holes look pretty rough.  One of the triple GUs had a 2' long scratch on the interior of the glass (this is the glass manufacturers fault but doesn't say much for the quality assurance on the side of the window manufacturer).

Are you doing the install or do they have a team?  I'd go out and take a look at some of their other installs and talk to customers who have their windows.  I'd also take a look at their warranties.  

I also bought windows from a local company but toured their factory.  I also specified the low-e coatings.  This was a higher end window company though and their product is/was great.

I've bought windows from the box stores as well - they seem good.  Typically you buy from a window manufacturer if you are after high performance and custom sizes.  The box stores are great for pricing if your window openings are sized for there in stock sizes.  

Cost effective and energy efficient kind of go against each other.  On a new build I typically go with less windows but bigger.  I find the best compromise is vinyl frame with steel reinforcement, triple pane windows with 366/180 on surface 2/5 and a 90/10 argon/air mix and a super efficient spacer.  Absolute best performance would be fiberglass frame, triple pane, 366/180 on 2/5 and a 90/10 krypton/air mixture.  3mm glass is quite thin so possibly in the future I'd opt for 4mm or thicker.  Also some 3mm is actually less than 3mm depends on the glass manufacturer.