The solution to getting optifine working with better skies if fairly easy!
Ok here it goes!
-Install optifine (and any other mods you are using)
-Download and run the Minecraft HD patcher
-You will get an error saying your minecraft is already modded, Ignore it and click OK!
-Now in the 1st mods tab turn OFF everything except better skies.
-Move on to the options tab!
-General options, don't touch anything
-HD textures, switch everything from Custom animated to DEFAULT
-Disable texture cache and the compatiblity fix.