Marcy,
Each one of the checkboxes are contained in a <li> tag. Example: the 'Technology Companies' checkbox looks like this:
<li class="mktField mktLblRight">
<span class="mktInput mktLblRight">
<input id="Technology_Companies__c" class="mktFormCheckbox" type="checkbox" tabindex="27" value="1" name="Technology_Companies__c">
<label>Technology Companies</label>
<span class="mktFormMsg"></span>
</span>
</li>
From <li> .... to ....</li> any padding or margins you edit will only edit THAT space reserved for that element.
If I understand your question, you might want to try and create a blank space (so to speak) between where the right most element closes </li> and the next element opens <li>.
This is the best advice I have for you. Possibly a new <li> which would contain its own width and height </li>.
Hope this helps,
James.