How bad is it to only have taken a max of 2 courses/semester in a premed post-bacc I applied to maybe 11 doctoral programs in neuroscience and biology last year and was rejected from all of them. So, I became very self-conscious (or even more self-conscious than I had been) about my science gpa and research experience. So, I decided to apply to and enroll in a post-bacc program for those planning to ultimately apply to medical or dental school, physician-scientist programs, etc. I myself am considering an MD/PhD or PhD to pursue a career in neurology and/or related research. In the summer of 2016, I only took one course, a neurobiology course (because very few of the courses I took as an undergrad were neuro courses while the majority were bio courses). 

In the following fall, I only took 2 courses. One was orgo (a retake) and another bio class. Now, this spring I'm in orgo II, a neuro class, and a mathbio class.

The challenge I'm having is that I flunked the first orgo II exam (was many SDs below the average) and the mathbio class is turning out to be super time-consuming because I'm really struggling to grasp the material. I need to decide whether to drop orgo II or this mathbio class soon but I really don't know what to do. My indecision is compounded by the fact that dropping one of these courses would just leave me with two classes total. I wanted to use this program to position myself as a more serious candidate but a consistently low number of courses per semester in combination with the less-than-hoped-for lab experience I've gained over the fall semester makes me look, I think, either afraid (afraid of taking on too much and failing so much so that I swung in the other direction and took so few classes) or lazy. Part of why I've taken so few courses is because I simply do not have the money for a full course load but part of it is because I really wanted to minimize the time spent away from studying orgo as I didn't want to retake something only to mess up in it again. 

I would really appreciate some advice!
I think you are paying too much attention to how others will interpret your workload and grades, and not enough attention to what you can learn from them.

The money issue is irrelevant because you would be prevented anyway from taking more courses because of the time you need to devote to orgo II and mathbio. You are considering dropping from three courses to two because of the workload, not to save money.

Something needs to change before you would be ready for a demanding graduate program such as an MD/PhD. The question you need to ask yourself is what are the reasons for the difficulty you are having handling three courses, and are those reasons something you can change in the future.

For example, if the problem were a full time job you could solve it by planning to be a full time student.

If you can identify a fixable problem you should do two things: 


Fix it ASAP, so that you can see and show what you can do with the fix in place.
Discuss the problem and its solution in your application materials.


If you cannot identify a fixable problem you may need to reconsider your career path to pick one that does not require the sorts of courses that are giving you trouble.