Both read & write drives support e-sata and USB 2.0, but my PC only has one e-sata port. Does the choice between using e-sata for read or write drive make a difference in speed? This is on Windows 7, if it matters. If there are any differences for Windows 8 or Linux, I would find that information useful also.
It makes a difference if the drive can write faster than about 35MB/sec. If it can not then there is no difference:
Basically you want to compare these three speeds:
The last can vary from about 30MB/sec (older 2½ inch drive) to about 100MB/sec (recent 7200 RPM 3½ inch drives to 200MB/sec (ultra high end 15K RPM SAS drives).
In your case:
If you have a very old drive it will not make a difference.
If you have a somewhat modern drive to a modern drive then eSATA will be faster for both reading and writing. You will gain the most speed by putting the faster of the two drives on the eSATA port.
I'd say to use eSATA for writing, as writing is generally slower than reading, and you don't want a double-bottleneck.
Why not copy files to your PC from drive 1 using eSATA, then swap in drive 2 via eSATA and copy them back?