the os and and another drive are in one physical drive while transfering from downloads, which is in the os drive, to the other dirve the data transfer rates are barely around 35-40mbps
This is 2 partitions on one physical drive.
wheras when i transfer from downloads to another physical internal hard drive the speed reaches 70-100 mbps
Yes, that may well be faster.
Drive 1 = 2 partitions, C & D
Drive 2 = 1 partition, E
Transferring data from C to D means the same drive heads are reading and writing.
Transferring from C to E means the heads on C are merely reading, and the heads on E are merely writing.