I have two collections:
Each upload has a User
associated with it and I need to know their
Populate() is just a query. So the overhead is whatever the query is, which is a find() on your model. Also, best practice for MongoDB is to embed what you can. It will result in a faster query. It sounds like you'd be duplicating a ton of data though, which puts relations(linking) at a good spot.
"Linking" is just putting an ObjectId in a field from another model.
Here is the Mongo Best Practices http://www.mongodb.org/display/DOCS/Schema+Design#SchemaDesign-SummaryofBestPractices
Linking/DBRefs http://www.mongodb.org/display/DOCS/Database+References#DatabaseReferences-SimpleDirect%2FManualLinking