I use Anki together with Wheelock's Latin (as well as any interesting Latin expressions I come across; no doubt I'll use it with Lingua Latina, too). What I do is I put entire sentences into my cards, like this:
Latin: Labor mē vocat.
English: Work summons me.
Usually I create both "production" (English -> Latin) and "recognition" (Latin -> English) cards. Sometimes I only create one when the other is too obvious (e.g., it's much easier to remember "Labor mē vocat" is "Work summons me" than to remember it the other way around), but Latin is difficult enough that I usually need both.
Occasionally Wheelock does have very long sentences that are difficult to abridge, and on rare occasions (only a couple of times in the entire book so far; I'm on chapter 32), I don't understand the sentence even with the translation. In either case, I simply skip it; I figure if I'll really need to understand the words or grammatical involved, I'll just encounter them again in a hopefully easier context. I also skip items that are redundant because all the words and principles are in other items, but if I'm in doubt, as I often am, I throw the sentence in, so I skip very few sentences.
I never just put raw vocabulary, principal parts, etc. into my cards; I let the sentences handle all that stuff for me. Occasionally I get thrown off because maybe the preterite or past participle of a verb isn't used in the book until some chapters later and I have a heck of a time looking it up ("What the heck is 'sublatus'?"), but it's a rare problem, especially since few verbs have completely alien preterite or participial forms.
I'd say this method has worked very
well, which isn't a surprise since I've long used this method with Spanish, too (though with Spanish I use production-only cards much more often, since many words and grammar structures in Spanish are easily recognized but not as easily produced.) It's sometimes difficult to read a Latin sentence even when I know all the words, but hey, it's Latin, so that's to be expected...