200Gb as slave and 20Gb as master - is this ok?

I installed a new hard disk of 200GB as slave and I can only see 137Gb which is grand for the time being until I upgrade the mobo etc. The master disk is a 20Gb ancient yoke. I read somewhere that the newer bigger hard disk should be master and the other slave. Is there any reason for this and will the bigger hard disk work ok if I leave it? My intention was to have the big hard disk for backups/storage and have no operating systems on it to mess it up. Will it be stable even though it can only see part of the disk? When using Win2k recently there have been momentary pauses in doing things that I never noticed before. I presume it is something to do with the new hard disk.