Okay, now it's clean, pop that collet up into the spindle, and hold it there with one hand (I use my left to hold it there, I find it's an easier reach for the drawbar in the next step this way). Reach up with the other (right, in my case) hand, and spin the drawbar threads down a few turns into the collet, capturing it and preventing it from falling out. Don't crank it all the way down yet, or you won't be able to get the cutter in!
Some mills use a protruding pin in the spindle bore to key into the slot on the side of the collet to keep it from rotating inside it's taper, so if it doesn't want to pop all the way in, try spinning it around until it easily slides in all the way. Our Jet mill here at menlo park techshop doesn't use one and the collet will pop right in at any rotation, but our older mills do, and will only slide all the way in when it's lined up correctly.
Don't panic if it doesn't want to slide all the way in, just rotate it around until it does!
But first, a quick note on *where* to grip on the cutter with the collet!
-the less tool stickout, the better! Basically, you want to use as short an end mill as practical for the job at hand, and grip it as close to the flutes as possible to minimize tool deflection, bending, chatter... Short = Rigid. BUT- don't "choke up" on an end mill and grip the flutes to 'fake' a short end mill! It chews up the collets, the tool, and is unsafe to boot. Don't do it!
So, you need to grip the round shank, somewhere above the top of the flutes, and below the groove / weldon flat (if it has one, but most do.) Take care to check all the flute lengths, I dug through our collection of end mills and found this classic example of one set of flute grinds extending farther up the shank than the other. You should make sure you're able to see the top of all grinds below the collet when it's installed. Or, to put it another way, you should see a solid ring of the shank between the top of the grinds and the collet. If you're using a cutter with a reduced or enlarged shank watch out for a chamfer or radius where the diameter changes, and make sure you're gripping on the round shank .
So, you should be gripping it somewhere between the second and third red marks from the left in the third pic, and between the two red marks in the fourth pic. Simple enough, eh?
A safety note is in order here: NEVER, EVER leave the wrench on the drawbar! If the machine turns on with it on the drawbar, it'll either twist the wrench into a pretzel, throw it across the room at somebody, or both! Just like a lathe chuck key, if your hand comes off the tool, the tool comes off the machine, EVERY TIME. Make sure you're not getting into the habit of switching hands with it still on the drawbar, or anything...
It's time to make some chips!
When you're done, to remove the cutter:
-pad the 'landing zone' with a rag again, just in case it slips!
-pull the brake and wrench the drawbar loose several turns, but still threaded into the collet
-tap the drawbar down with the mallet side of the wrench to break the taper, drop the collet down, and spit out the tool... Don't forget to be holding onto the cutter with your other hand while you do this! If it doesn't spit it out, spin the drawbar out another couple turns, but make sure it's still threaded into the collet at least a turn or two. If the threaded end of the drawbar is sitting on top of the collet threads instead of engaged with them, you can bugger up the first thread on your collet, or heavens forbid your drawbar threads!
Have fun, and be safe makin' chips!