We're not clear what you mean about having to edit hundreds of products? Our Shipping Rules are cart-wide regardless of product(s) ordered, rather than product-specific, and you can set min./max. order weight thresholds to enable/disable a Shipping Rule in the cart. See more details here:
Your suggestion of having a different shipping container for the First Class product(s) could work, or you might consider just setting up a Shipping Rule using our "USPS - Cheapest Available" method, which is the same as our old USPS live rate-lookup method -- this obtains the rate for First Class and Priority and applies whichever is cheaper for the order's weight and destination. This will normally result in a First Class rate for orders under 13 oz., and Priority for orders above 13 oz., as First Class is not genearlly available above that weight.