If I am adding query string parameters to one of these, should I put my own "?" there or should I assume AdWords will figure out if a "?" or a "&" is the appropriate separator? I should add that I am modifying the URLs for a third party and do not necessarily know what values are in the URL fields for their keywords.
if you're dynamically creating landing page URLs, they're not URL data pairs, so construct them normally without those characters (but there are special cases where your URLs might have appended data pairs in their construction).