Answer 1

Programming for controllers may be C (I also saw some prep packages in C#), but linking where I found that is firmly in the blackhat arena so...here's how a businesses might go about it.

~ Usually you just buy a controller for the memory chips you plan to use -- you don't need to know what's in the controller -- then you become a manufacturer for that combination of controller + memory.
~ But...if you approached a company making controllers, interested in working for them / what should you study / you may be able to work out the answer with a controller manufacturer.

Here's a product page for a manufacturer that makes several flash controllers:
http://www.siliconmotion.com/A3.2_Partnumber_Detail.php?sn=22

You might want datasheets (this is how you'd integrate), but getting those legitimately probably means "be an OEM", affiliated with an educational institution and/or sign NDA/confidentiality agreement.

To identify the vendor/product (VID/PID) for a device you have, try 'lsusb' for Linux-like systems.