I still don't know what you man by the white boxes, but I will take a guess and assume you mean the section editing windows. Here are two things you can do. To set a maximum height for the sidebar:
div#dokuwiki__aside {
max-height: 40em;
overflow:auto;
}
To set a maximum height for the section edits:
div.levle1,div.level2,div.level3 {
max-height: 20em;
overflow:auto;
}
The 40em and 20em are just suggestions. Experiment to see what you want. These go in conf/userstyle.css. You can use one of these or both. Note, however, that if the content of these containers exceeds the height of the containers, you will ge scrollbars.