I have been using VSD 5.7 but am considering switching to the latest version. A couple of questions...
1. Do I unistall the first then install version 5.9
2. Are when I open up my site within the new version, make some changes, are there any problems I need to be alerted for that I might run into from what others have experienced?

I am happy with what I have but the new version sounds like it has features I would like to take advantage of
thanks

If you have a choice, wait for another week or two. The current 5.9.1 has upload problems when using the built-in FTP as reported by others; I personally use a separate FTP software so had not encounter that, but have run into some other snags that made me wish I could go back to 5.8.5, but one could NOT once saved using the newer version ...

The register.exe will fix any issues there. The big difference for 5.9.X series is the syncing. You no longer have to re-upload everything. The core component of the ftp though is the same since the 3.0 series however.