Order of taking courses I take my courses in a very specific sequence which I believe maximizes my learning potential and enjoyment. Unfortunately, that means that some key 'checkbox' courses I am to take might be put off until senior year. Will grad schools assume that I'm just not taking them at all? Or will it be OK to take them even as I'm applying?
If you are applying to graduate schools while you are still enrolled as a student, you will normally be asked to provide the most up-to-date transcript you have at the time of the admissions process—and may have to provide a mid-year report if a quarter or semester has elapsed between the time of submission and the decision date. So, the only courses the school may not see may be the ones in which you enroll after such a mid-year report. 

Now, in general, if you're not leaving too many classes until the very end (in other words, the "standard" load for someone in the field), there won't really be any questions asked—people know that different departments have different ordering and sequences for classes. However, if you are leaving "standard" courses normally taken earlier in the program for the end, you may need to explain why. However, your local academic advisor should be able to guide you on whether this will actually be necessary for your particular case.