This is not a direct answer to the question of partitioning a flash drive, but there's a better solution. Create an encrypted disk image file and put that on the flash drive. Store all your sensitive files in there. This works on all Macs without the need for any third-party software, though not on Windows machines. So if you need to access that data from a Windows machine as well, you'll need to find another solution.
Thanks for your response. Yes I had thought of that and it could be an option as presumably I can set the size o fthe encrypted disk image and leave a portion that is not password protected?
I'm not so worried about any data being stored in the encrypted disk image being readable by Windows, so long as the portion left (though not password protected) could be viewed, copied from on a Windows machine.
One last Q, so the encrypted data is safe on all platforms. I.e if I lost my USB and someone with Windows tried to access the data they wouldnt be able to?
You can not only set a size for the disk image file, you can also make it a "sparse bundle" that is capable of growing as necessary to accommodate whatever you put in it. Much better than a partition.
And yes, the data is secured on any platform. If you lose the flash drive, there's no way with current technology for someone to decrypt that file and get your data out, unless you choose a weak password that they are able to guess.