With so much variation in the data layout of CSV files, it tends to take some tweaking of the Import Options to get everything to fall where it should. It sounds like you are importing a field other than the Amount in to CheckBook's Amount column--this would explain why all Entries show up as one color or the other since the color is based on whether an amount is negative or positive. Also, if the stuff you are trying to put in the Amount column is text and not numbers you will get zero amounts.
If you feel comfortable sending us your CSV via email, we could tell you exactly what to set for the Data Layout from the Import Options. It could even just be a few lines of transaction data if you'd prefer. Just attach it to an email to
support@splasm.com if you would like us to take a look at it.