You're best upgrading the alternator wiring although in truth you'll probably get away with the standard cable as the chances of the alternator putting out 100A for any sustained period is pretty slim !
The resistance of the cables is the most important factor with winches (or any high current 12v system) and for that reason I'd never use welding cable as normally it has a much higher resistance per meter than battery cable. If you want to know why, there follows a "short" explanation of how winch motors work
When you activate a winch motor you are, to all intents and purposes, putting a direct short circuit across the battery, through the motor. The only resistance, and therefore the biggest limiting factor in it's performance, is the resistance of the cables and joints. The only reason the motor doesn't melt as a result is that as the motor spins it generates/induces eddy currents in it's own windings that limit the current flow, the faster the motor turns the stronger these become and the less current can pass through.
It's this effect that limits the speed of the motor as the combination of the eddy currents induced into it's own windings and the resistance of the cables determine the speed the motor can run at. As load increases and the speed of the motor decreases the eddy currents reduce allowing higher currents through the windings and increasing the power.
As you can probably surmise from this, the most damaging thing you can do to a motor is stall it and keep it activated when it's not running because in that condition the only limit on the current is the resistance of the wire. So if you ever hear the winch motor stall, stop winching or you'll burn the motor out !
Welding wire is used with a higher voltage normally where the voltage is increased to control the current that flows. As a result welding wire has to be capable of taking the current but it's resistance really doesn't matter in that application so it's resistance is often quite high when compared to battery cable, often sacrificing low resistance for flexibility.
At full chat a winch motor on a standard low line winch will be pulling close to 200 amps and at the most you're probably going to get between 11-12 volts to push that through. You can forget 13.8 volts because the moment you try and pull more than 100 amps the voltage will fall away. At 12 volts the absolute maximum resistance of all the cables and the motor windings and the battery and the connectors is 0.06 ohms. Adding even 0.01 ohms to that in your cable will reduce the maximum current (and power) of your winch from 200A to 170A and the figures get worse as the voltage drops below 12v.
In summary - get the lowest resistance cable you can find of a suitable current rating and use that ! In battery cable normally the higher the current rating the bigger the cross section and the lower the resistance.