Should I store my code/projects on my SSD or my secondary drive?

SSD have a much better IO and therefore it makes sense to have your code on the SSD disk.

It depends on the drive you have. The read is will always lose to the SSD, but maybe not on the write performance. Write performance is going to be important during compilations for creating new executables, assemblies and other build artifacts.

Copy one of your larger solutions to the HD and the SSD and compile both. You'll notice the difference one way or the other and have your decision. My guess is the HD will be faster for compiles/builds but the ssd will win everythig else.

I don't know if this is possible in Visual Studio, but the best may be a combination of the two. Put the source code on the SSD, but have the compiled objects written to the HD. This is how we have out make based projects layed out, but for other reasons.