Should I enter new Square items into Craftybase first or the other way around?
It is recommended that you always create your products on Square where possible and then import them to create as products in Craftybase. This means that your external references will be correct from the start and you will not need to do any merging between your manually created products and imported ones.
Alternatively, it is possible to create your products on Craftybase first if this works best for you. Once you have your product created on Square you should then import to create the new one in Craftybase. Be aware that this will create two versions of your product as the importer will not yet know about your manually created product. From here, you will then need to merge together the two products so that all orders and purchases are under the correct product. All imports after that point will know to associate new sales and expenses to the correct product, so this will be a one-time task.