Ah, I see; wasn't clear what you meant by overlap. The size of the box it self is very restrictive and you'll need to increase that too. Please see the below CSS needed.
Code:
.connectionBox div[style~="top:18px;"] {
top: 30px !important;
}
The above is another situation where classes are lacking so a bit of CSS trickery was needed. Other adjustments may need to be made to expand the box. This can be done much easier with CSS3 selectors, but don't advise using them until IE8-9 is more widely used; other browsers don't have issues with CSS3. Please note the important tag (doesn't work in IE6, but no longer an issue these days) is vital as in-line styles always have higher weigh then class styles; without the tag the in-line will just override your CSS.