Are there any guidelines for how to distribute images in a (bachelor) thesis? I am preparing my Bachelor thesis (it has to be around 20-25 pages long in case it makes a difference) in Biophysics and I want to put some images at the very beginning as a way of introducing and making clear the physical processes and systems that I'm going to consider through the whole thesis.

I am writing my thesis using LaTeX and a one column style and I don't really know where and how to put the figures. For the figures that contain results of simulations and similar things it is easier because I can almost always put two of them together so they cover the whole width of the text, but if I put a schematic drawing of some process I feel that there is a lot of blank space around. 

What I have done so far is to change the style to two columns in that part of the thesis and use one for the image and the other one for text. Is this acceptable? What is usually done to avoid having a lot of blank space around the figures?

Also most of my figures are interspersed thorough the text (I am using LaTeX automatic positioning so far) because I feel that it is easier to understand the process if the schematic figure that I'm referring to is next to the text. Should I continue doing it or should I put all of them at the end of the section or of the whole thesis?
The basic guideline for this should be your institute's guideline on how to layout bachelor or master thesis.
From a typographic standpoint you should never mix one column with two column layouts. LaTeX offers packages which you can use to wrap text around figures to reduce white spaces.
Like you said and did, I also would put the figures around the spots where they are mentioned in the text. LaTeX arranges them automatically (you can however specify some positions in your figure environment). But from my experiences, it does a very good job at finding the right positions.