Bootstrap comes with a grid-like architecture that will allow you to create sections in your page so that they all line up and stack appropriately. Become familiar with this first and then assign the right classes to each section. For example:
col-lg-12 is will create a section 100% wide.
col-lg-11 will create a section ~90% wide
...
col-lg-6 will create a section 50% wide
and so forth.
So to create the right placement of your divs or sections. add a row class to every section that is stackable.
If you are having two sections side-side inside this row, add a col-lg-6 to each and they will line up next to each other and on top of each on mobile.
Now, to the obvious problems that I saw right away.
Between your body tags, create a wrapper class div that will contain your page and define it's width.
Do not use so much positioning. Specially position:fixed. This is what makes things sticky and messy. You wan to make use of your margin, padding, floats, and displays properties to properly align things.
Give it a try before I hand you any code. I want to see your brain work first. Then we'll trouble shoot some more.