I already installed Windows 10, using the Boot Camp Assistant, on my MBPr (late 2013) without any problem. However, it is a "new" model, everything went fine.
But, now I am trying on an iMac (late 2009) and the process is a little bit harder.
The Optical Drive was replaced by a SSD, so I needed to change the Boot Camp Assistant to accept ISO images]1. Now, the Boot Camp Assistant creates the Windows USB flash drive installer.
But, on boot, the flash drive is not visible. If I just wait, the message "no bootable device" appears, so I guess it went looking for the Optical Drive – so I restart one more time, pressing ALT so I can select the flash drive and… It is not there! (Just some "EFI something")
If I insert the flash drive on my MBPr, it can find it and Boot as it should be, so the 'problem' is just on iMac.
Ps: I am using a Windows 10 ISO, that theoretically has no drivers for this iMac – but I think that this is not the answer for the flash drive do not appear.
Best Answer
Update #2
I see you were able to successfully install Windows 10 by modifying the procedure given here. At some point in the future, I should replace this answer with a procedure similar to what you followed.
Update #1
In my answer, I did state that I would need additional information before recommending changes to the steps given. Apple has published that you can run Windows on a second internal drive, but you can not install Windows on the second drive. Apple recommends removing the first drive, installing Windows and then reinstalling the first drive. This is not a practical solution for MBP users.
I still have no more information about the partitioning of your internal drives than when you first posted your question. However, you may wish to try this older post regarding installing Windows: How do I install Windows 10 on MacBookPro5,1, with no optical drive (SSD+HDD)
Orignal Answer
Apple recommends using an USB optical SuperDrive to install Windows when the internal optical drive in unavailable.
Even though Apple documentation states a late 2009 iMac does not support Windows 10, this may not be true. I installed Windows 10 on my mid 2007 iMac. In fact, this post was entered using Windows 10 on this Mac. Generally, you should install using the latest drivers issued for your model Mac.
Installing directly from the iso file is possible, but the process is tedious. You also have to install free third party software. The steps would be similar to the answer given here. Of course, you do not have the standard OS X installation configuration. I would require addition information regarding the partitioning of your internal drives, before recommending changes to the steps given.
If interested, submit a comment below.