The mites migrated to the eyes and heat pits because of the "soaks" you do.
Like its been mentioned, if you have a spray such as "Provent a mite" , you treat the cage, and the mites will die eventually.
Now... You want to run it by the vet to make sure that whatever else he has given you or making you use will be safe in conjunction. The poor snake is weakened with all it is going through.
You always want to be careful to use more then one product when getting rid of mites or external parasites. You CAN overdose that way. Usually you should stick to one product at a time, esp. if it contains permethrins or pyrethrins.
When it comes to mites I prefer sprays such as provent a mite, where you treat the enclosure and it kills the mites on the snake.
So read the instructions and ingredients on the items the vet gave you, and if any have a "lingering" effect, then wait for a bit.
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