I have registered Renoise but one thing I am a bit confused on is when updates are put out, do I just replace the files in the zip with the files I already have or should I download the latet trial every time and install that first before I replace the files?
both are true.
most of times, when upgrading to a major new version (1.1 => 1.2), you will need to uninstall previous version, install the new trial version before, and then overwrite it with the registered executable; when upgrading to a minor new version (1.25 => 1.26), overwriting the executable is sufficient.
Anyway, you will find, time by time, the proper info about this in the download page in your user page: just give it a look to it (it is written in red, normally)