I'm asking because i'm about to finish RTK1,and i want to create two decks,one with sentences and another with Vocabulary. I'm going to get the sentences from this books,Understanding basic japanese grammar,200 Essential Japanese Expressions: A Guide to Correct Usage of Key Sentence Patterns,and 500 Essential Japanese Expressions: A Guide to Correct Usage of Key Sentence Patterns. I know these books have furigana, and i can double check the furigana Anki generates. I want to get the Vocabulary from the net,for example this webpage http://japanese.about.com/library/blvocaburary.htm
As you can see the vocabulary don't have furigana only romaji. This seems to be a problem for me because, some time ago i try to enter some sentences i got from the net(they came with a sound clips too)i was reviewing the sentences and listening to the audio clip,but the furigana anki generated didn't match, i know i enter the sentence correctly, but i wasn't sure if that was the correct reading or furigana. I don't want to add romaji to my vocabulary cards just to make sure they are the correct reading, it just seems too noob, well i know i'm a noob, but it just looks kinda embarassing. Sorry if i'm not making sense but my english has gotten a bit rusty.

Anki rarely messes up furigana. Counters (日　匹　本）, names, and certain expressions or obscure kanji/vocab are what give it trouble.

It frequently screws up words like 開く (ひらく) and 開く (あく) and other cases were its non-trivial for a computer program to get the reading right. I'd recommend checking the reading of anything you add, at least until you're confident of that stuff yourself. If you have the romaji, that's all you need to be able to check and correct the furigana.

Do you always rely on spell-check to proof your documents without error?

Of course not.

Kanji with multiple readings, especially days, numbers, counters, as well as certain characters (私, for instance) and verbs that have multiple readings often are generated wrong.

It's pretty accurate, but trust me, double check it if you're not sure. You don't want to drill one reading into your head over thousands of hours only to find out that it's the wrong one.

I only check reading for cards that I cannot get correct audio from Audio Download. If I get it correctly I don't bother doing anything and assume that reading was common enough for JDIC to include/record audio for it.