Well, reading/writing to/from both partitions on the same disk is always great fun. I only ever put multiple partitions on a disk if I plan to never exchange data between them, such as dual-booting scenarios. It's just a taboo I've had since the early millennium, when I never really understood everyone's obsession with partitioning the crap out of a drive.
There's not that much difference between reading/writing to/from two partitions on the same disk and reading/writing to/from data on the same disk that I can see, assuming you partition wisely.
But... why exactly are you still partitioning your discs like that for? Is it really just so you can have a partition, instead of a folder, with your data?
There's plenty of reasons to partition a disk - ease in data backup, simplified reformat/install of the OS, better performance for certain activities (OS and apps in faster portion of drive, placement of swap file away from other data, etc), and others I can't think of off the top of my head.