I can't illustrate with pictures at the moment, so you're going to get an Oregon Trail type of post here. OOooo your imagination will get to work.
I use these inserts:
http://www.amazon.com/dp/B0026GUEN4/ref=biss_dp_t_asn and 3/4" #6 machine screws, which I trim to size ex post facto.
When you are looking at your single coil route, you will notice that the rounded sides accommodate the drilled ends of the pickup. To properly locate the pilot holes, you can simply center the pickup cover within the route, ensuring that the rounded edges are centered within the lateral ends of the route. Take a chassis punch or other pointy object and mark the spots while you hold the cover in place. Remove the cover and drill your pilot holes.
Now, with the thickness of the body in mind, you will have to calculate not only the the depth of the threaded insert (which should be flush if possible), but also the length the machine screw will have to travel to offer an acceptable range of height adjustment. I use a single bit, sized appropriately for the threaded insert, and take it down
about a half inch further - you must do the math so one of two awful outcomes can be avoided:
1. You drill through the guitar body
2. You do not drill to a sufficient depth and, having prevented adequate machine screw travel, you snap off the head of the machine screw, mar your new body, and nearly punch a hole through your work area into an adjacent room where your fiance may or may not be watching the Bravo network.
Having drilled to a sufficient depth, you will gather an insert in hand and do the following in the absence of a threaded insert tool:
Ignore what appears to be a slotted screw driver receptacle. If you are confident, orient that end downward so the shearing force from the "install tool" will be evenly distributed along a single, continuous surface. One one occasion, I have used that slotted end to remove an insert, but if too much force is applied it will shear. This was during one of my first attempts.
Before I drilled the main insert channel, I selected the appropriate bit by ensuring it was the same size as the insert's body. If you go any smaller, you will rue the day you were born. Incidentally, you can go a smidgen larger, but most drill bit sets have course jumps in size from one bit to the next, so you will most likely disregard this. I have never needed to use wax or any other lube to seat the inserts. These are made of soft brass, so consider how essential sizing the bit is in the process. When I'm home later this eve, I'll try to see if I have documentation around the bit size.
Now, take your 3/4" machine screw and see how far into the channel it can go before bottoming out. If the head or thereabouts is above or just below the route's deck, you are in business.
At this point, I grab 2 #6 nuts and thread them on to a shortened screw and then thread it onto the insert. You do not want to see too much of the machine screw exiting the bottom of the insert or it may bottom out and cause a most grievous outcome. See outcome #2 above.
This unit has just become your install tool, but you must remember that you are dealing with soft metal in not only the insert, but the screw itself, which will not withstand much torque at all before shearing at the head. See: Outcome # 2 above. It is critical that you select the ideal driver tip to avoid stripping the head.
Take the insert assembly and position it onto the channel and start driving it. Be aware of the feedback the driver is giving you. If you feel the effort has become reduced by a fair margin, stop and back it out. You've ruined the machine screw and it will likely shear. You should have consistent resistance all the way down. Once the insert is flush, unscrew the machine screw and it will leave the insert in place. Be aware of your driver! It will be almost touching the side of the pickup route, so be careful that you do not damage the paint.
Rinse and repeat.
You will now take a bit slightly larger than the machine screw and you will drill your pickup cover and the pickup bobbin to allow a little margin once installed. This margin will allow you to overcome a slightly less than perpendicular channel. The #6 machine screw will be wider than the pickguard screw, so that will ruin its use for that method of attachment. Might as well go a bit wider.
I use high density foam to act as a stabilizer/spring. I have also used the rubber tubing on the machine screws in conjunction with this when the mood strikes me. If you cannot lower your pickups to the desired depth, do not over tighten! You will break the machine screw! You WILL. See outcome #2 above. Simply remove the machine screw and nip off a bit of the length.
I am not responsible for you! You must measure!