When you talk about uploading in phases, would I test a plugin then install it onto my live site
That is how I would personally do it. (I develop only WP sites full time)
it could run the risk of deleting a new user who had just signed up
There would be nothing to "replace" on the live site if this is a new plugin. When you install a new plugin the plugin will perhaps "add" options, meta fields, or even create a new database table, but it won't overwrite your existing values for things like users or post content, etc. unless the plugin specifically tells you in the install directions.
If I install Contact From 7 on my TEST location, then alter my CSS to make the form look good with my theme, I can then upload that plugin to my LIVE site and also edit my LIVE CSS files with the new changes. This particular new plugin will not change any existing entries in my database so anything that happened while I was working on this (new users added, etc.) is not altered.
large plugin based features that I know will require database modification.
Properly programmed plugins are made to "adapt" to your site. Again, this could be adding tables or just adding custom fields.
If you are getting into member plugins or forums, then these will, most likely, add tables and also add user roles or capabilities in which case should walk you through setting them up properly. For example, the plugin won't "remove" users or change a user's ID, but it might have you select a new role for subscribers during setup.
You can even swap your entire test database with new LIVE database if you really want to see the exact effect. (That is somewhat advanced.)
The main thing is to read all the plugin install directions carefully. Most will walk you right through it with basic options in the admin area. The plugin will(should) warn you about any changes that could affect database entries, etc.
This goes without saying but do select a plugin that is well-maintained, current with WP versions and has a good review from other WP users, etc.