Does Mnemosyne have any features that Anki doesn't? It's been a while since I've checked, but when I first switched to Anki from (shudder) SuperMemo, Anki looked better than Mnemosyne in every way (or at least every way that matters to me). Maybe there's something I'm missing, though, and no doubt for some people the difference isn't important anyway.
I'm wondering how it is you're currently using Mnemosyne. What I do with Wheelock is I simply make English -> Latin and Latin -> English cards using all the Latin sentences in the book (I get the English translations from the official answer key), without making vocabulary cards or cards asking about conjugation or anything, and so far it's worked perfectly fine for me. I've also long used this method with Spanish, Italian, and Japanese, and Japanese is the only language for which this method has proven problematic. (I need to figure out what to do about that...) I don't feel like I'm "learning how to take a test" at all... the only thing about Wheelock is that the sentences often feel very contrived, but the further you go into the book, the less that happens, I think.
My main concern is that vocabulary-only items don't help you develop reading skills. The free word order of Latin makes it notoriously difficult to get used to, but if you keep reading Latin sentences and see how they work, it's easier to get used to the ones that are complicated or use unusual word order. (But don'tcha just hate poetry that starts a line with an adjective, and doesn't put the noun it modifies until the end of the next line?) Using sentences with your SRS ensures that you'll be doing this even when you're not actually reading.
Still, my method's only one way. There are plenty of people who do it differently or don't even use an SRS at all, and their methods work fine for them...