I buy mealworms for my gecko. The small ones and the large ones. Only giving the large ones as a treat.
I just keep them in the boxes that I buy them in but was wondering whether I could tip both of them together in one bigger box/pot.
If they're all really mealworms and the large ones are not superworms, yes, you can keep them together. You may want to investigate getting some better gutload "food" for the mealworms so they're more nutritious for your geckos. Most pet store mealworms aren't packaged in anything very nutritious. You could do this by getting different grain and unsweetened cereal and powdering them (so it's easier to sift out mealworms) or you can get chicken feed from a farm store.
Yes, you should keep them separate. ALso, mealworms can be refrigerated to slow down their metabolism and rate of changing into aliens, but the superworms will die if you refrigerate them.