I would be the last to say that you can't partition it manually - but - what I will say is that if your partitions do not match what the unit expects, both from a structure and content point of view (configuration files are stored in one of the partitions), then the unit may, at some time, prompt you to reformat and possibly reformat the "other disk".
The scripts that handle the partitioning and formatting of the disks appear to be the most troublesome area of the unit, I won't claim to understand them, in fact, at times I think even the developers don't understand them (there have been reports of the unit incorrectly formatting the other disk - not the one the user is expecting to - and despite several firmware upgrades, the problem seems to remain).
In short - go right ahead and try - but make sure you back up your data.