I use Superior 3 as well, and my approach is probably closer to yours. I'll occasionally use the loops that come with it as more-fun metronome tracks for jamming or practice, but in my own music, I program them by hand in the Reaper piano roll. Pros - huge amount of flexibility, and if you put the time in, with Superior 3 you can make it very, very realistic sounding. Cons - you have to put the time in.
My workflow is basically to start off by creating a single drum loop or a couple if the different parts of the song have markedly different drum parts, in my head, and track against that. I'll usually start with a pretty simple, straight beat, pretty much all the major hits as I want them for the "riff" I guess of the drum performance, for lack of a better word. Next pass would be taking those loops and bringing them to life a little - adding snare ghost notes, say, or if it's a one measure loop maybe gluing 2-4 of them together and having a longer loop that corresponds to a discrete "chunk" of the verse or chorus with different patterns here or there, maybe a few extra snare or kick accents before the repeat, whatever. Then, vary up intensity a little, perhaps, at the micro level - I try to, if there's a hi-hat bit driving the performance, try to vary that organically a little with the beat, within the loop, or maybe have a partially closed hi hat open a little more selectively at different points. Then, I do the whole thing again at the macro level - should the verse performance be a little softer than the chorus? Or, the first verse a little quieter, then hit a little harder for the second? Select all your hits and adjust velocity a little for these sections, so the drums aren't all playing at the exact same intensity throughout the entire song. Then, once I have a good flow on the "macro" level, where the drums sound realistic in discrete sections, and respond to the overall dynamics of the song in realistic manners, I'll go through and start splitting out parts of those loops and then editing them to create fills. This can be very time consuming, in part because the difference between a programmed-sounding fill and a realistic sounding one can be as simple as slight changes in note velocity.
I'm a pretty bad drummer, but I've spent enough time behind drum kit over the years that as I'm working I'm thinking about things like "with two hands and two feet, could a human being realistically play what I'm writing," and "how hard could a drummer realistically play this hit, given what the rest of their body is doing," and stuff like that. Spending some time behind a drumset, if you haven't, will REALLY help your programming... but if you can't, then the thing that helped me a lot was trying to recreate the drum performance, in the MIDI roll, of recorded drum parts of songs I like. You'll learn a lot doing this, and then over time you can just listen to a drum part and think about how it's likely being played and save yourself the trouble of doing it the hard way, while still learning.
