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I have heard there can be an allegory inside another allegory (mise en abyme), but what about 2 concurrent allegories (at the same time) and how do you insure that people don't get confused by the fact you employ different symbolisms for 2 different allegories concurrently instead of one after another?
How would you do this?
Think of Wizard of Oz, but with 2 different allegories being told concurrently instead of 1.
There are no rules. Many people read and enjoy stories without looking for or considering allegories. Heck, the Wizard of Oz is supposed to be an allegory for the politics of the 1890's, who watching it or reading it today would catch on to that? Nobody, but the story continues to be told.
Your story has to stand on its own without any allegory. It has to be clear, and enjoyable, and satisfying to finish. If there are one, or two, or five allegories in it, great, but do not count on the allegories to be what sells your story, to agents, publishers, literary critics, or the public.
For some authors, I understand, the allegories help them organize and complete their book. So go for it. If two embedded allegories gets you through the 1000 hours of work you have to do, use them. But above all, make sure your story holds together and doesn't stall out if the reader doesn't perceive any allegory at all.
Amadeus's answer is great if your goal is story-driven-story. IF however, you're working with something more experimental, I think the nested allegories can work, just like a musical leitmotif for one character can also have a musical phrase that echoes the adventure theme.
Margaret Atwood does great work with this. In The Robber Bride, one of the characters is a history professor, and she figures out historical battles by using seeds and spices on a topographical map, and they also are reflecting her antagonism with other characters. One of the characters changes her identity to suit the other ones (for good or ill), so there's all sorts of complexity going on. https://en.wikipedia.org/wiki/The_Robber_Bride
In The Blind Assassin, the story takes place over different time lines, and in one time line there's a story about a pair of lovers, one telling the story of the "blind assassin" (an explicitly invented story within the story), and there are echoes of the lovers' relationship within that as well.
https://en.wikipedia.org/wiki/The_Blind_Assassin
In general, look to poets-who-are-also-novelists (or vice versa) to get a sense of these possibilities. But I look forward to whatever you come up with!
If I'm understanding you correctly, you need a story that can be readily perceived at three separate levels simultaneously. First --as in Amadeus' excellent answer --it needs to work as its own, stand-alone, compelling narrative. Second, it needs to represent something different --for example, the 2016 presidential election season. Finally, it needs to represent something else yet again, for instance the psychological journey from childhood to adulthood.
It's difficult to think of any actual examples of this. Perhaps the Platonic dialogues, or the parables of Jesus. Maybe some of Kierkegaard's writing, or the stories of Chuang Tzu. In terms of full length novels, the only book that comes to mind is Lewis Carroll's Sylvie and Bruno (but that's more a case of taking three separate narratives and just mashing them together). Samuel Delany's Dhalgren might also be doing something like this, but if so, the underlying allegories are not clear. The same goes for Murakami's work. That suggests you'd be breaking your own new ground in doing this.
Personally, I'm attracted to this type of writing experiment, but in my own experience, the storytelling has always suffered from having to carry the weight of too much symbolism. If you're determined to do this, my advice would be to do as I hinted at above, and make the two allegories very different kinds --not both about historical incidents, for instance, but one of them being more literal, and the other more psychological.
