Can a lease cover seperate parcels, although adjacent, in different counties?
Yes. Even different states. The lease will need to be recorded in each county to impart constructive notice to innocent purchasers (there are a few exceptions to this, such as would occur in Texas under this same situation).
As an aside, there is no advantage in having non-contiguous tracts of land on the same lease and there are many disadvantages. My suggestion is to pretty much always have non-contiguous tracts on separate leases.
I have a interest in 45 acres that is in two different quarter sections. I have heard that it would be in my best interest to lease each seperate quarter section. Doing this supposedly would make it unnecessary for a pooling clause. Would one lease suffice for both quarter sections?