I was talking to the maternity benefit people recently about a similar situation (history of PAYE employment, then jobseekers benefit, then self-employed, then paye + self employed) They told me you can qualify for the MB in two ways (as long as you have the right history of stamps - which you have ).
1. If you are a paye worker on a contract (whether or not you are also self-employed) you can apply for MB to start the day after your employment finishes, so long as you are at least 24 weeks pregnant at that stage.
2. If you are self-employed you can also qualify if you are earning enough from the business to be liable for a prsi contribution the year you are taking maternity leave. I think this means you are earning over €5000 in reckonable income. They will take your word for it that this is the case, then check the following year when you make your tax return and if you shouldn't have got the MB, you will be asked to repay it.
In your case it seems quite straightforward- you can qualify in the basis of your PAYE work as you were told.
MB is taxable from 1st July this year so as far as I understand it you will be taxed on a combination of your PAYE earnings, income from your own business and the MB you receive.