I absolutely suck at music theory, I can play scales instinctively but I can't put a name to any of them and I don't know how to use them.
Scales are used in creating melodies. Basslines traditionally outline the chords but can be melodic in nature (listen to late-period Beatles and classic Motown). In other words, scales are a lot less important to basslines than many people seem to think. Soloing...OK, they are more helpful there.
Assuming you are talking about rock songs: Unless you are deliberately trying to play a melodic line, the first beat in a bar should always be the root of the chord, that's easy! It should also be the lastnote you play at the end of the song, hey that's really easy!
The next most important notes (in order) are the fifth, then the third and seventh...
the chord tones. There's about 999 million basslines that use nothing but those notes. Anything blues-based (including funk and a lot of classic rock) will work fine using nothing else. Playing only the root, fifth and flat seventh (in the key of E, that's E, B and D) in various permutations is one of the most common sources of basslines in rock. Avoiding the third means you don't have to deal with major vs. minor, that's a load off your mind! Everything else in the line pretty much revolves around rhythm, especially syncopation.
Here's an example in classic rock of three songs that share the same basic figure in the bass line. Notice that at first none of these sound like they have the same bass line.
Why not? Because they have totally different grooves.