You don't actually need any theory here. You should experiment with what you have been writing, and see if it sounds good. If it doesn't, you'll need to change stuff.

Now a diminished scale can be (in whole and half steps) WHWHWH etc.... (the whole half diminished)

or HWHWHW etc.... (the half whole diminished)

Now if your first riff is E F# G A A# Then I guess your going for the Whole half diminished

For the second riff you've got E F G G#, that's E half-whole diminished (keep in mind that every note in a diminished scale could be the root, although the form might change). If you are going for B diminished whole half, this is the correct scale.

Now it is perfectly legal to have both of these scales in your song for your riffs, although I would make some kind of transition line, maybe with chromatic notes.

Yes you could make the bass fill in E minor, but again I would make some sort of transition, say a guitar or bass letting out the b5 right at the end of the measure.