Everything can be done in in DirectCSS. Here's some references to IDs and Classes that might help.
For cart popup size:
#cart_view, #unitprice_view
the table (box) within:
.cart_containertable
Your logo: more likely there's a link to it into this block:
#generating_progressbar, #unitgenerating_progressbar, #design_vrml_progressbar
This would also be the block defining the size of your progressbar boxes