I would NEVER go to a 'manual' alignment shop. It should be done always on a laser alignment rack. As for getting the car aligned to particular specs? That is a lot harder to do, but your best bet is check with some guys that autocross locally, see where they get their cars done at. Autocrossers typically want more toe in, or toe out, (depending on FWD, RWD, or AWD) to improve turn-in, or steering response.
If the car is used as a daily driver? Toe specs should be set to factory, really, all specs 'should' be as close to factory as possible at all times. If you've lowered the car significantly, then it may not be possible to get camber and caster in range without the addition of a camber kit, or other suspension modification.
So, to clarify, yes get it done at a shop with a computerized alignment rack, to factory specs. Seting the car to factory specs is preferred, unless the vehicle is autocrossed, or road raced.
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