This is all assuming you have gotten as many beta readers as possible. This is also assuming you have a firm idea of your own artistic goals and personal style and have no problems saying "no, thanks." I'm not saying "write by committee," I'm just saying that to understand any large group--such as a whole target reader demographic--more data means more accuracy. So, provided you are confident in throwing out obvious outliers and things you don't like emotionally and personally, it's more helpful to see if 19 out of 20 people agree, instead of having two critiquers who disagree and no other 18 to weigh in.
Assuming you want to take that route at all, here's my advice for how to sort the resulting feedback.
1.) Make everyone talk to each other.
The reason I built the Ubergroup the way I did is because I find it helpful to have everyone hang out and have a round-table discussion. It's modelled on rehearsals for any sort of performing art. Music, dance, theatre, circus, it's all the same idea. You do your thing in front of your troupe and then they all pitch ideas at you, debate and discuss.
I find that a lot of times, people who seem to being saying opposite things in their crits were actually just using different phrasings. When talking directly to each other, and one person says, "I have to disagree with your suggestion in your crit of chapter xyz, because I think..." the other person often says "Oh, yes, that would work, too. My suggestion was just another way to solve the same problem."
That takes all the stress out of going "But person A said this and person B said that!" Having person A and B hash it out directly eliminates conflicts that were simple misunderstanding. A and B are often attacking the same problem from different angles, and discussion may lead to consensus.
So, have everyone discuss together. I usually end up with something like 9 out of 10 people agreeing, and the 10th person admitting graciously they might just be the outlier. On the occasional thing where it's a split 5-5 vote, then I know I really have to look into the subject further. Knowing which topics are so divisive is also helpful.
(Also, who doesn't find it hugely flattering listening to people debate your "literary themes"?)
2.) Sort the everloving shit out of it.
I just finished sorting through the massive 20-page discussion thread from my last beta round, picking out all the salient suggestions and sorting them by general topic. I know know that sounds like a lot of work, but I find it even more work to jump around as I edit. If I change a scene based on one person's feedback, then I stumble across someone else's related suggestion on the same scene like 5 discussion pages later... guh. I hate having to re-edit a scene a dozen times because someone else made a really good point. It's far less work overall to paste all the suggestions on the same topic together, and think about it at once.
It's important to add that I do not leave any of the conceptual ideas in the crits only. As I'm reading the crits, I bring up all the suggested conceptual changes in the dedicated discussion thread, and everyone opines. If there are 10 crits per chapter over 30 chapters--300 crits--Lord help me if I'm supposed to poke through the whole unsorted pile for a vague idea somewhere. I'd much rather copy-paste each individual comment into groups organised by topic the first time I read it, and never have to go through the whole mess again.
It takes about a week, but eventually I condense all the ideas.
Here's the part I think people using the Ubergroup's beta method may find particularly helpful. I bold each general major conceptual issue so I can easily skim through in search of a topic, and then paste together everyone's ideas. For ease of reading, I don't copy parts where people are saying things like "Yes, I agree!" just the sentences containing actual suggestions.
In practice, it looks something like this:
Edmund/John conversation about death and John scolding him for holding onto the dead: "Does John secretly blame Edmund for their mother's death? Does Edmund resent John parental attitude all the more because he just lost his mother as well as his father?” (Laura R) "I think it would be pretty nifty if there's a scene somewhere in the first half where Edmund attempts to talk about their parents with John, just to kind of vent and grieve together and John's totally cold and "We must let go of the dead". " (Dahlia) "It could even be another moment where Edmund don't feel he can be good enough." (Raven) "I never connected the religious 'don't mention the names of the dead' with why their parents were never mentioned. So this talk would show there's a reason why they aren't discussing their dead parents, not just that they aren't thinking about it/don't care." (Catherine)
3.) Think about what I agree/disagree with.
With all the suggestions together, it's easy for me to consider all the opinions on one topic without fear of overlooking someone, look to see if there's any majorities, and decide whether or not I agree. That's important:this is not "writing by committee." I value all 5, 10, or 20 voices, but I'm the director and tiebreaker. So, I decide, and then implement the conceptual changes.
4.) Reread all the crits again.
After I've made all the conceptual changes, I do re-read all the crits again at the very end, looking for line edits. Skimming for highlighted typos, word choice issues, etc.
Hopefully that's helpful to some of you. It's one way of keeping track of an epic-scope project, at least.