Help, which end boot should I install, 4x12 or 2x12?

Depends on location of the vents, climate, system type - heating, cooling or both and heapump vs furnace for heat if applicable.

2x12 is very small for 6" metal. you do lose a bit of area to the register/grill.

I would go 3x10 or equivalent if you need good throw.

4x10 or 4x12 if you want lower velocity/noise.

Ok, so here's as much info as I can come up with, my furnace is natural gas, it is approximately 40 feet away, I live in MN, will change out furnace as soon as I get duct work installed,no heat pump, basement room and room above is to be supplied with heat and a/c, no returns in either room. both rooms will be supplied with 2 lines of 6inch round.

How did you determine what each room needs in terms of supply?

Basements need less heat than main floors yet both get the same amount of heating/cooling? Why?

Vent locations?

I would use smaller registers for heating the basement (2" wide too small though for 6" feed) if they're in the ceiling - want to force the hot air down so it can properly mix, not just have it trickle out and rise to the ceiling.

Return air near floor is important when heating registers are in the ceiling.

If you're heating previously unheated areas, keep in mind you can starve existing rooms of sufficient supply air if the trunk lines are (/trump line is) too small.

the rooms are approx. 368 sq ft, upstairs (master bedroom)will be coming out of floor register, basement (theater) will be supplied from ceiling and soffit.

home depot rep. said I would need two 6" lines to each room

i think i just uploaded pics

Ignore the guy at home depot.

Sizing is not done by sq ft.

The basement probably doesn't need much heat.

Why does the master bedroom not served by the central system? How is it heated now?

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It takes calculations (how much heating/cooling do the rooms actually need?) and assessment of the existing duct system/equipment (how much airflow does the furnace need?) to do this properly- you can really mess up your system just adding runs.

Four 6" metal pipes flow a lot of air, your trunk lines may not be large enough to add that much and other rooms won't get proper airflow.

electric baseboard heat, no a/c, this portion of the house was an addition, heat in on dual fuel meaning the power company shuts it off when they feel like it and then there is no heat. that room is a walkout basement on a lake with the wind coming off the lake, theater used to be a tuck under garage.