Clip the Leads
DANGER
Wear safety glasses!Wear safety glasses! Clipping leads often sends them flying unpredictably.
Hold one or two leads with one hand, and use your cutters to clip them free with the other hand. Holding them will not only greatly increase your safety, but will also make cleanup easier.
Clip the lead, but not the solder. You'll have a little dome of solder on the circuit board; It shouldn't be flush.
Save the clipped leads for additional practice when you run out of resistors.
FYI
Some people recommend you clip the leads before soldering. This helps prevent undue stress or impact to the solder joints that may jeopardize the integrity of the connection.You can certainly try this, but it makes assembly a bit trickier without a special PCB holding rig to keep the components in place. In practice, it's very hard to damage a solder joint by clipping the lead anyway. Also remember we're building a guitar pedal and not a space shuttle, so the risk is probably acceptable.