Ok, great! So the 1.87% equine horse paste is often apple flavored which squirrels don't seem to mind at all.
Knead the tube with your fingers to try and more evenly distribute the active ingredients. Take a drop sized amount of the Ivermectin paste (slightly less than the size of an uncooked piece of white rice) and apply to a shelled pecan piece (you can use other treats but the ridges in the pecan are useful for holding the paste). Give to squirrel (try to toss near him so he gets it). Not a very scientific dosing method but it has worked safely and effectively countless times.
Wait about 7 days and repeat this process. In some cases a third dose after another 7 days is helpful.
The first dose kills the live, adult mites. The second dose after 7 days will kill newly hatched mites (Ivermectin does not work on the unhatched eggs). #3rd dose at 21 days is just for good measure.
You should see new hair growth starting in about 2 weeks or so after the first dose. Poor little guy must be miserable, glad you can help him!