You haven't said what type of section break you have, or why it was placed in the template.
Section breaks typically are inserted so that the page layout for page-breaking section breaks or section layout for non-page breaking section breaks, can be different before and after the break.
You can apply page layouts, such as margins both before and after the break.
If you started formatting the page after the section break was inserted, the formatting applied will not automatically apply to the pages before and the pages after the break.
Without knowing the details of your template, I suggest that you place the cursor in the section that is not formatted as you require, and apply your margins etc. using the same settings before and after the break.
Section breaks will move as text is added before them. You can't make a section break stay at say the end of page 1. If you add text to page 1, the section break will move, eventually being at the end of page 2 and so on as more text is added.
I can't say what effect removing the section break will have. Just save a copy of your template under a different name and remove the section break and compare both versions.