I currently have a Maxtor 7200.10 320GB HD
and am planning on buying a WD 6400AAKS HDD.
Which should i use as the main drive (which will perform faster?)
Not knowing much about the Maxtor 7200.10 320GB (which i surmise to be similar to Seagate 7200.10s since Maxtor is a subsidiary of Seagate), I would estimate that the WD 640GB would be faster, as many benchmarks point them out to be supremely fast due to their two-platter design.
The Maxtor may very well be a single 320GB platter inside as well, which would make the performance equally comparable in theory, as the platters in the 640GB (2 x 320GB) would have about the same areal density as the 320GB. Whether or not the two-platter design is somewhat slower because of mechanical design, I have no clue, unfortunately.
The WD is going to much faster, if my memory serves me correctly the maxtor uses a two 160gb platters. The WD use two 320gb platters the higher data density will result in higher throughput. WD drives are also usually better than Maxtor
It's best to make the fastest hard disk as the OS drive for the best "zippiness" with loading applications and other hard disk I/O related applications (such as booting) in your OS.