How can I discuss a salary increase with my boss while also
acknowledging how much they've done for me already?
How about something along the lines of the following, during a 1-on-1 session between you and your boss:
"Hey boss, I've been meaning to talk with you about something.
I truly appreciate all that this company has done a lot for me,
including paying for me to take classes and giving me a substantial
raise in my last performance review.
I really enjoy working here, and really like working with you.
I've gone from essentially a data entry position to overseeing two
development projects without a large salary increase, and yet I feel
that I add more value to the company than my salary currently
reflects.
I'd like to get a raise. What can I do to make that happen?"
Then take it from there and see what kind of response you get.
This basically expresses your gratitude explicitly, while also asking for more money.
Note that you have indicated you already got a "substantial raise", yet you also say that you've gone "without a large salary increase". To me that's confusing - substantial but not large? You probably want to clean up that line of thinking a bit before your discussion.
You also haven't indicated where you are on the salary range for others in your role (perhaps within your company, or within your industry and in your locale). You may already be right where you should be, or you may be significantly under where you should be. Knowing more about that could strengthen your argument.
And of course, enter the discussion being prepared in case the response is "No". Decide in your own head what your next step will be (nothing? look elsewhere? quit immediately?). I don't suggest anything rash - just that you have considered all the possibilities.