I am surprised no one has answered this for you.
On the Mac, I would recommend to do everything separately with the best program or tool for the job. Create your pictures by hand or by a drawing application. Create your graphs in Maple or elsewhere. Analyze your experimental data in a spreadsheet or something else. At the end, generate PDF files, either by direct print to PDF or by scan to PDF (at an appropriate scanning photo-copier). Finally, use Preview to assemble the pages in to one continguous document.
On Windows ... hmmmm ... I would be lost at the moment. I would still recommend to do everything separately, then generate individual PDF documents. I _think_ you have to use a third party software (eg Adobe Pro) to concatenate the separate files ... I am not sure that Windows comes out of the box to handle such effort (as per Preview on the Mac).
As to the template, I might suggest to have a title page that you change from assignment to assignment. Everything else gets copied in behind that title page. This would streamline the document creation process.
HTH, even at this late in reply.