Depending on whether you went from one manufacture to another some programs might not be fully functional and will require a reinstall. Usual when you clone it'll copy everything successfully but the odd time you might have some missing .dll files and so on.

I am curious as to how to make the SSD my primary drive

is your ssd currently your C drive?
Usually when you install a program it'll let you select the path to where the program installs to, this is usually something C:\Program Files\. You should be able to select your secondary drive and install your programs there.
If you have existing files on your boot volume you can move them with a program called SymMover, I've used it a few times and have never had an issue with it. It's really simple to use.

As for "locking" your drive? I'm too sure if theres an easy way around this, the best thing I could suggest it just to use your pc and when you need to save or install programs just point everything towards your secondary drive, eventually you'll have enough preferences on your pc for it to automatically save files to your secondary drive.

right, but I do not want anything on the SSD besides my OS. How do I move everything that is not my OS onto the HDD and still maintain access to the files

Two ways two easily do it.
First way, transfer everything to an external hard drive until all that's left is Windows on the hdd and use a cloning program to clone hdd contents such as Windows to ssd. ( You can use TodoEaseUs)
Second way, set the ssd as primary drive in bios and clean install Windows onto ssd, that way hdd won't be wiped!
Good luck

Ceiling wrote Two ways two easily do it.
First way, transfer everything to an external hard drive until all that's left is Windows on the hdd and use a cloning program to clone hdd contents such as Windows to ssd. ( You can use TodoEaseUs)
Second way, set the ssd as primary drive in bios and clean install Windows onto ssd, that way hdd won't be wiped!
Good luck

I've already done the fresh install. I think I got it working by having to switch the program files over via rereg or something like that.

I've an idea

install the os on the drive, go to disk management, shrink the drives partition down so the drive only has 40gb free space. You should always have free space on an SSD, since it's flash memory that's where the drive does it's processing.

Once you have partitioned your drive you'll be forced to use your secondary drive. Just save and install everything to the secondary drive.

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This is a great tool that's pretty widely used in the IT world, but it's not free.