How can I be sure to only get one enchantment per item?

You can enchant books instead, which always puts only a single enchantment on it, and then use the book in the anvil to apply it to a tool or weapon. You do have to go through a lot of books to get exactly the enchantments you're looking for, and it costs extra to transfer the enchant from the book to the tool on the anvil, but what you get for the loss of efficiency is precision in having exactly the enchants you want.

Note that you can also combine enchanted books of the exact same level on the anvil to get one book that has that enchantment level +1. So, you can take two Efficienty III books, combine them, and get one Efficiency IV book as the result. In this way you can slowly gather together the pieces for your ideal set of magic tools and, with enough XP lying around to go through this XP-inefficient process, get a set of tools to your precise specs.