What is the best practice for having a global collection or set number? I am setting up a content type for a collection of samples. There is already a lot of samples that have a collection number that can't be changed, so I will have to import that data. But My question is how to apply this number; I know its a broad question, but would using taxonomy, or a field in the content type be better?
A field would be better if the collection number must be unique. If so you can activate the Unique Field module to enforce it, then go ahead and import your existing data.

If it does not have to be unique, either will work, but I would still recommend using a text field rather than a taxonomy.