Be patient with nominations. Give people an individual nomination limit (depending on how many rivalries you want it). If a day or two and nominations aren't going as fast as you'd like, increase it a bit, then wait again.
Typically for things like this seeding is done based on how many nominations each thing get (more nominations=higher seed). Beyond that you could seed them yourself based on what you think will do the best (ex. Mario & Bowser would probably be high seeds), or just randomize.
As far as bracketing, I personally prefer Challonge > Bracketmaker because Challonge does data entry and seeding for you. If you have them ordered from highest seed to lowest seed, you can just copy and paste it and have it automatically seed the bracket. Bracketmaker works fine but you'll have to do the seeding yourself.
Once the contest is running, find a set time you'd be available each day to update it. That way it just becomes part of your daily schedule and keeps the topics to 24 hours, preventing people being upset that some matches get more or less time than others.
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Khal Kirby, warlord of the Super Star Khalasar PSN/Steam: CheddarBBQ https://goo.gl/Diw2hs