Yes it matters. They should be marked, but if not, put your multi-meter on voltage across the two wires with the panel facing the sun so there is some voltage.
If you have pos to pos, the meter display will say, eg 34.2, but if you have neg to pos, the meter display will say - (minus) 34.2. So now you know which wire is which, put some red sticky tape on the panel's pos wire.
1. 1991 Oakland 28DB Class C
on Ford E350-460-7.5 Gas EFI
Photo in Profile
2. 1991 Bighorn 9.5ft Truck Camper on 2003 Chev 2500HD 6.0 Gas
See Profile for Electronic set-ups for 1. and 2.