Activate the “include in view layer” checkbox in the outliner and use that to hide original collections without disabling them from rendering. However, it is annoying if you have various incomplete projects or helper objects that you always want to remain hidden (eyeball). Whenever you re-enable that checkbox it forces ALL objects within the collection to become visible again, so annoying.
Because of that problem and the annoyance of things overlapping at [0,0,0] I just make the things where I want them initially, parent them to an empty, and use the empty location as the instance offset value. Moving the collection contents is not a problem as long as I remember to change the instance offset value to wherever I moved the parent empty to.
or
What I’ve started doing lately is putting the collections I want to reuse into another scene named “assets”. Make a 2nd scene. Open 2 outliners set one to “Scenes” mode. Drag the original collection into the 2nd scene. Right click the collection in the main scene and “unlink” to unlink it from the main scene. Place a collection instance in the main scene.
If you have 2 monitors you can open 2 blender main windows [ Window > New Main Window ] and show the main scene in 1 window and the assets scene in another window. You can edit the asset in the 2nd window and see preview renders of the main scene in the 1st window.
Yes these are all annoying workarounds that should be formalized and named and documented. Whenever I go back to old projects it’s always a mystery as to what combination of the above workarounds I was using in that scene. Moving forward I’ve decided it’s best to annoyingly document such information in the blend file for the future.
If there was a way to tell the collection to automatically always have a relationship between the instance offset value and the empty I parented the collection contents to, it would save a lot of time.