Why and when do I use 12-bar blues? I know it's used with pentatonic and blues scales, but people like Jimi Hendrix, John Frusciante, and many others use pentatonic and blues scales with other chord progressions for example little wing or voodoo child, so how do they derive chord progressions from pentatonic or blues that are not 12-bar blues?
There seem to be crossed wires here, with respect. Blues progressions basically use 3 chords, I, IV and V. True, often dominant 7ths, but that needn't muddy the water for now. There is a recognized order to the sequence. Actually, almost any notes can be (and are) used to create solos over these sequences. It's just that lots of the time, guitarists in particular, like to use either the minor pentatonic scale notes, or them with an added b5, making the blues scale notes, over the blues. It's not obligatory - some use the major pent, or major blues notes, which also work well. Others will mix and match.
Any three chord structure can use those same notes, or others, at will. There's just a different order to a three chord song that isn't a 12 bar blues - even if it has 12 bars in it.
Yet again, looking at the sequence from, say, Hey Joe, which certainly isn't a 12 bar, and certainly not a 3 chord song, the blues scale notes can be made to work in it, but one needs to be careful which notes get favoured over any specific chord. But that's actually the trick with any solo: one can't play any old random notes from a blues scale, and sound good! Some work better, some worse, over a particular chord or sequence. Listen to someone who's just learnt a blues scale play a 12 bar, and it becomes apparent!
The last bit - chord sequences aren't just derived from a set of notes (a scale).