There are numerous causes for eye discomfort upon awakening. Bedroom ceiling fans are a major culprit. You need to see an eye-MD for a comprehensive dry eye and blepharitis evaluation. There are many specific causes of blepharitis and dry eye, and this diagnosis is too complicated to be sorted out on an internet forum. Once you know exactly what is going on, check back for helpful practical advice on lifestyle changes and treatment options.
I think you have blepharitis, as I have that same feeling upon waking, and I have been diagnosed with it. Just google blepharitis, and you can learn all the wonderful facts.
Once in a while I develop a chalazion due to the blepharitis. Even though I use exceptional eye hygiene, use an antibacterial eye ointment, consume lots of flaxseed (recommended by my Dr. and good for everyone anyway) and use hot compresses regularly, I still average one a year. I was on an oral antibiotic for a while, but it didn't seem to make much difference and didn't want to keep taking it indefinitely.
I don't know much about the eye drops you are using, but my Dr. has recommended Zaditor (I got a coupon at zaditor.com) The drops really aren't for the blepharitis but more for allergens, which can add to the discomfort. The CVS brand worked well too--shop around for the best prices.
Good luck!