From a technical point of view, you have several options: Remesh, Dynamesh, Booleans, ZRemesher or manual Retopology. For some, like Booleans, you'll have to split your Mesh into separate subobjects first and for ZRemesher probably one of the other options to get a solid, non-intersecting mesh. I'm a bit rusty, but at this stage, ZRemesher would probably be a good option, and if you're nearing completion, manual retopology, taking the link Eric supplied into consideration. You might also want to split the eyes to a different subtool unless this is for a statue of sorts.
Trying some retopolgy might help because the topology does not fit the wish to connect those parts. Also if there would be some loops around the eyes as suggested by multiple tutorials for good topology then indeed it would be very easy to connect those because the loops would align to the circular eye lid topology. But then there is a reason why i wrote this in subjunctive.
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http://wiki.polycount.com/wiki/FaceTopology
I'm a bit rusty, but at this stage, ZRemesher would probably be a good option, and if you're nearing completion, manual retopology, taking the link Eric supplied into consideration.
You might also want to split the eyes to a different subtool unless this is for a statue of sorts.