It’s not a problem at all. If you are playing with a Neck pickup of any Target Guitar, through the bridge pickup of your Source guitar, the sounds will be anyway close to that on of the Target Guitar in the bridge pickup position. However, the Emulation works in the best realistic way by matching the source and target guitar pickups. For this reason, the pedal automatically assigns the Neck pickup of your Les Paul to the Neck pickup of a Telecaster target guitar. This means that when you want to emulate a Neck pickup of a Telecaster (true to the original) you should switch the pickup selector of your Les Paul to the Neck position.