I know mine is the C7 vs a C6, but with a S-Line on 18's, my suspension is not as smooth as my dad's old C6 SE, but it never feels harsh/crashy... only real complaint about mine is that it it so composed and carries such effortless pace everywhere that it never feels that fast.
Definitely don't buy a car based on the wheels, similar for the suspension, if anything an SE on aftermarket suspension will be more pliant and better handling than an S-Line, but just bear in mind that a SE on aftermarket suspension will (a) still be an SE (bodykit, seats, and value/appeal on resale) and (b) be a modified car, so more expensive to insure. Personally I'd go with the S-Line from the start just becuase I prefer the exterior styling and I've converted a previous car to S-Line body kit (my old silver "Sport" B6) and it was NOT cheap!!
18's are fine on mine, but not sure I'd be keen to put 19's/20's on it though (I think the optional upgrades go up to 21"!!!) and even for my winter tyres, 18's are the smallest I can go due to the brakes... I think most C6's can go down to 17's for winter wheels, so if it's on those, keep the old wheels for that!
And I'd second that on the remap... I've always been in favour of TDI's with a moderate economy remap as a minimum, "fast road" preferred for manual gear boxes, but I'd go with a milder remap for an auto: make sure the remapping company knows what they're doing and doesn't release so much low-down torque that it ruins your clutch.