How exciting!
DH and I got married at the local courthouse in 2007 - we'd intended to marry when we could afford it but my Catholic upbringing kicked in when I was pg with DD1 and I felt the urge to 'get legal' before bub arrived, so we decided to have a courthouse wedding while pregnant and do the big party thing later on.
You can download the relevant forms ('Intent to Marry' or something like that) from the BDM website, it cost us $175 to lodge the paperwork and the ceremony itself cost a few dollars more (all up, under $300). When we lodged the paperwork at the courthouse, they told us it was a minimum 5-week wait ('cooling-off' period, if you will) and we were able to book a date that day (when we lodged the papers).
We invited just immediate family (my parents, DH's parents, my nanna and our brothers) and rocked up on the day, the ceremony was all over with in about fifteen minutes and DH's dad and my dad acted as our formal witnesses.
After the ceremony, we went around town to different scenic spots and took heaps of photos, then had dinner at a local restaurant and DH and I stayed in a motel that night with a spa so we could treat ourselves We bought a cake, but didn't worry about flowers or any of that stuff, all up including rings and a nice dress it cost us about $1000

We really enjoyed it, it was a very intimate, low-key wedding and we could just be ourselves. Made it legal and now we're looking at doing a 'proper' wedding with the big white dress and huge cake and reception with all our friends present on our 5th wedding anniversary

Good luck with it, I think registry/courthouse ceremonies can be great if it's what's going to suit you and your beloved, I definitely wouldn't change my lovely little wedding! Best of luck to you both!