Yes, they were given equal weight.
So for example, if Sleepless voted for JP and Scoot, and Lottery voted for only Scoot... that's 2 votes for Scoot, 1 for JP.
I counted the bonus votes separately on the opposite side of each entry (trust me, it was intuitive) so I could see how many main votes and bonus votes something had at any given time. When it was time to choose the runner up, the main votes and bonus votes for that nominee were all counted. It was interesting to see how the Master voters would pull one nominee ahead of the others.
This also means we didn't assume The Master would win anything. By distinguishing the type of vote, everything was given a chance to beat The Master. Which didn't happen.... not even in the poster and trailer categories.