Something along the lines of the best day of your Union will be counted for the scoreboard, and then will be ranked according. So if you do 721 Experts on one day and 511 Ults on another day, then your Union's scores will be 721 Experts and 511 Ults.
Ranks 1-5 in Experts get 5 SR Grails (meh), 15 R Grails (meh), 1000 Jewels (okay). So Experts don't really matter at all, really.
Ranks 1-5 in Ults get 15 Dragon Eye Shards and 1000 Jewels. 6-15 12 Shards, 1000 Jewels. 16-30 10 Shards, 750 Jewels. And so forth.
There's also individual PP, which is the highest amount of PP people have done in a single day. However, personal PP is above all something that your Union helps you achieve, so these spots will pretty automatically go to the high performers of Expert and Ult runners. Not to mention that a single Union hosts 30 people, so top5 Unions will have 150 people on them...
In theory, you need a good, coordinated Union do well.
Practically, if MMOs have taught me anything, cheaters will entirely dominate the leaderboards. And Nutaku doesn't exactly have a track record for caring about those