Hi ambientproject,
You should be able to completely override the CSS for the edit bubbles from your own stylesheet, but it's not something we recommend, as long term we might be adding new items to the bubbles. However, if you do the CSS right, even this shouldn't be a problem:
The CSS bubbles are defined here:
http://cms.pagelime.com/linked/css/cms/editable-page.css
In the /*new bubbles*/ area.
You can inspect the structure of the bubbles via firebug.
So - to override the bubbles your style would have to be like this:
body.cms-page-editor-preview .cms-bubble { /* your bubble style */ }
Notice the BODY class - this is a class that PageLime adds to your body tag when your page is in the CMS editor window, so you can use it to create conditional CSS that appears only inside pagelime.
In fact - you could use this to add spacing to the areas that are causing a problem on your page! You could do something like:
body.cms-page-editor-preview .my-small-element { padding:10px; }
To add some padding while the page is viewed in Pagelime.
Hope this is helpful.