Now that your insertion tool is prepared, you can start installing the inserts on your instrument. Here's a Further guitar without any holes for mounting the truss rod cover:

With the plate in place, drill the 3/32" pilot holes:

Remove the plate:

Drill to 1/8" finished hole size:

Load threaded insert on tool. Notice the orienation of the "slots" - they are the entry end of of insert (and opposite of the way you made the tool):

Use the allen key on your tool to install the insert.

It's okay if you install them a little deep - the screws will still reach them, but it looks nicest when they are near flush:

Some notes: do not use any glue on the installed insert unless the hole is too large. Even then you must be extremely careful because if you get glue on the interior threads, your machine screws won't be able to enter the insert. When you are making the insertion tool, allow the glue to dry for a good hour before using. Even though it looks like you could use a screwdriver to install the insert, it was not designed for this method. The tabs on either side of the slot cannot withstand the force of insertion.

It's also not a terrible idea to practice on a scrap of wood before taking this to your precious instrument.