In my experience Net Direct rates do not affect upgrade chances, others may disagree.

Always ask...
Place an upgrade request in the Comments field of your Reservation (online) and then ask when you are checking in.
While some think they should be given the upgrade without asking or reminding the check-in person that they are elite status, I have found that just a simple reminder or "Were you able to get me that upgrade?" works wonders.

Example request for Comments field in Res form:
HHonrs Gold VIP guest would like a room upgrade if available.

Also, this isn't directed at you specifically but mostly for the benefit of all the newly minted Golds... if you read through several of the first pages of this forum and/or use the Search function many of your initial questions will be answered.