Submitting two related manuscripts at the same time to two journals I have two ideas (manuscripts) that I am working on, both in the field of physics.

The first is theoretical, mathy and generalized. It is steered toward computer vision. Probably if finished, would be published in a multidisciplinary journal for physics and computer science.

The second is a mix between theoretical physics and experimental physics. It is steered toward astronomical physics only. It applies one of the results found in the first manuscript.

Is it ethical to submit these two papers separately? How can I cite the papers if they are both under peer review?

Note: The two manuscripts do not hold the same goal and do not have identical results. If I am going to put a percentage on how much 2# uses from 1#, I would put 20%. Further, if I would put a percentage on how much different 2# from 1#, I would put 90%.
Is it ethical to submit these two papers separately?


Typically, yes. Having a methods papers and one (or more) applications paper isn't at all uncommon. 
It's sometimes appropriate to send them to the same journal (or same publisher), but that is more a matter of convenience than ethics. If you submit both to the same publisher, they might ask the same reviewer to referee both papers, for example. On the other hand, if one paper fits better with the scope of another journal, then sending it elsewhere is the appropriate choice. On the ethical side the only potential concern I see is that you might be perceived as "salami slicing", i.e. spreading a small amount of content into multiple papers, but if both papers are "meaty" enough then that shouldn't be an issue.


  How can I cite the papers if they are both under peer review?


In the fields you mention, it is standard practice to put preprints on the arXiv. The best approach for you would likely be to do exactly that before submission to the journals, and then cite the preprints as appropriate.