Advice please, on organising user projects for a new user

I can't knowledgeable speak to the preset/customize issue. I do know that some  presets are kept per project other presets are global. Others will know better on this.
 
My project folders are kept in a separate drive E:/ with each project folder having it's own audio folder. That way a single backup is all I need to save every project.
Look under Preferences-File locations for specific file placemet locations
 
All my samples files (Garrititan, Kontakt etc) are kept in an external hard drive.
 
 
 
Fred
 
 

The guys above already referred to this..
Reading your question I wondered, what do you do with the audio.

Sonar is a bit of a mess when it comes to file organisation. The most comprehensive route is to go into the Folder Locations section of the settings, and make sure all those locations are backed up. If you're lucky, they'll only refer to 2 different places - Cakewalk Content, and Users\YourName\AppData\Roaming\Cakewalk\SONAR Platinum\ - which makes it easy to manage. Also, make sure you're saving audio with the projects (meaning the Global Audio Folder in the Audio Data settings page should always be empty.)
 
Unfortunately Cakewalk Content contains a load of irrelevant static data that you don't change and which can be re-downloaded from Cakewalk for free, so if time or space is at a premium, exclude Cakewalk Content/Audio Library, Cakewalk Content/Video Tutorials, and Cakewalk Content/Sonar Platinum/Tutorial Projects. Typically 80% of Cakewalk Content is in those 3 directories and they're not files you change, so you don't need them in your backup.
 
Don't forget to consider backing up your VST paths - many plugins will not work if not reinstalled properly, but some will, and the others will act as placeholders to remind you of what you had installed before, at least. You may also want to back up any external sample, loops, or presets directories that you have - I put all these under a common top-level directory to make this easier.