Boot Camp flash drive not showing on boot for late 2009 iMac
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.