"Wondering whats best for winter leg protection,pants or baselayer like R1 bottoms?And synthetic or down and what brands?thanks"
I think it depends on whether you are on the move or sitting around camp.
R1 and other heavier base layers will very likely prove too warm if you are exercising strenuously. My own personal preference for hiking is Under Armour Cold Gear Base 1 or Base 2 under a wind pant, in my case MH Transition Featherweight Pants(no longer made). There are many other equivalents out there, but the idea is break the wind and transport your sweat outward. Around camp is where you will want more insulation, again with a wind barrier. Lots of options