That's the way I do it, the parallel allows you to use both without having to use two different output jacks. Alternatively, you could put it on a switch. The cap keeps the signal from heading that direction anyway, so it doesn't give you any 'tone loss.'
Also, if you're ordering from smallbear anyway:
Http://www.smallbearelec.com/Detail.bok?no=986There's also a way to buy the alligator clips individually. That pack from Radio Shack would do fine if you needed something, but it's for a pack of ten. If you just need 3 or 4, buy them individually from Smallbear for .39 each. I advocate getting the pack of wired clips personally. The wire's already attached, it's durable, and now you have a bunch of extra wired alligator clips you can use for connecting other things together. Handy for testing random LED's that may or may not be burnt out, or attaching a Battery to something in a pinch, or making sure your jacks are grounding when outside of the enclosure without having to solder a wire in there.
I don't recommend the prebonded wire, especially if it's only 24 gauge. It's probably not flexible or durable enough because it's thin and prebonded. I recommend at least a 20 or 18 gauge stranded wire, and you should reinforce the connection with some heat shrink so it stays strong. Your weakest link will be the connection to the jacks and to the alligator clips if you do it yourself.
Jacob