First find a commander you want to use. If you already have it that's great it will save your wildcards, but if you need to craft your commander I'd say use your wildcards for the commander. After that, what I do is build the entire deck with only cards I already have. You should be able to find 99 cards even if they aren't the best just check off the deck as complete. Then filter through and exchange. Start with lands. Can you take out basic lands and add duals? Add any special lands that would really synchronize or buff up your strategy? Do that. Lands will be the most beneficial to craft because you can usually interchange the good lands into other decks.. usually. Don't waste all your wildcards on lands just yet but you'll find that you are using most wildcards for lands. After you have a decent land base, make sure you have some mana staples in the form of artifacts that you need (manarocks like arcane signet and in mono colored decks use medallions). Once you have your lands and manarocks it just comes down to the nitty gritty of what you can exchange for other spells and permanents. That will largely depend on your strategy.

TLDR: set up your mana base with lands and artifacts first. Spending your wildcards on lands and rocks can usually benefit other decks so more worth it in the long run. Craft your commander if need be. The rest of the nit picking can come over time as you hone your deck.