Can I have both my supervisors write reference letters?
I've sat on my department's graduate studies committee during application season, and so I can provide at least one point of anecdata for how PhD application recommendation letters are used, at least in my tiny corner of the academy. YMMV.

First, These letters are among the last things that are looked at. We don't have rigorous thresholds for grades, GRE scores, subject GRE scores, publications, etc. But all of those things are used to "objectively" sort the pool. First the obvious admits are skimmed off the top, and fellowship offers are made to some of them. This is the first place where letters are important, since quotes are mined from those letters to try and win funding for these students from the University (i.e., we entice the student with a prestigious award, and the department doesn't even have to pay for her!) The money quote is usually a ranking and/or direct comparison -- "In my twenty years at Giant State University, I've seen no more than 5 students of X's caliber. I would say her talents remind me of Y's at that age, who is now a professor at Prestigious U" -- and this is why even a mediocre teaching letter is more useful for this purpose than a nice letter from a PhD student (who can not be counted on to have a reasonable intuition for another's future potential).

Second, we work our way down to the marginal cases; this is much more difficult since the marginal cases require a more holistic take on the application package. No one gets immediately thrown out just for bad grades or a bad subject GRE score, but we expect some explanation of a mitigating circumstance (not an excuse!) in the personal statement, and hopefully reflected in the letters as well. For example, if you were dinged in the first pass for a low GPA, we would like to see that it was a bad first year (and not a bad fifth...); that you are on an upswing. If you think you might be a marginal case for whatever reason, the letter from the PhD student might be helpful -- perhaps you don't have any publications, but the PhD student can vouch for your work and verify that you have something in preparation, or explain why your project failed (projects often fail!) but that nonetheless you mastered some state-of-the-art technique on the way.

On the other hand it is a big waving red flag if those things are then not pointed out by your actual boss (the PhD holding supervisor). If you think the student will write a better letter, then you're probably best off having that student lobby on your behalf with the professor, to make sure the professor's letter is strong, and then get a second letter from someone else.

I would strongly recommend you do not ask for a letter from a non-academic unless it was an actual research position (and even then, these can be iffy if the supervisor has no letter-writing experience). On occasion we see glowing letters from a student's supervisor at their summer construction job, or a call center for a political campaign. Well-rounded students are great, but such letters are almost useless.