I just want to know if I should split this question into three different sections using "%%" or if I should just lump the whole thing together.
It does not matter to MATLAB. Some people find it easier to do debugging if they use %% seconds, but I find it to be more of a nuisance myself.
The one thing I would point out is that using %% is more likely to get you style points.
Do I put fprintf in three separate sections or just at the end of the whole problem?
It does not matter to MATLAB. However, it most of the time, people find it easier to read code that does outputing quite soon after computing the values to be output. There are, though, definitely cases where you are looking to create a formatted "report", and in such cases it often makes the most sense to compute the values and then call a report-creating function to create the report.