I would assume that you will just be dealing with the day to day bookkeeping rather than preparing the annual accounts - as the bookkeeping side tends to be quite straightforward, whereas preparing the accounts not so and in my opinion should be looked after by an accountant.
I do the bookkeeping for a charity and they use Sage. The main difference is where they have restricted and non-restricted funding. That basically means that some of their funding can only be spent on certain costs that are stated when the funding (grant) is given. For example, they may receive funding from a foundation that is for a new office. The charity can spend the funding on items relating to the office and nothing else. Whereas another amount received might have no restrictions and can therefore be spent on anything.
It's this element that can be fiddly (not difficult) as you have to make sure all costs are allocated correctly so that under/over spends are accounted for, as some funding is given on a use it or give it back basis.
The charity I work with has the majority of its funding on a restricted basis so I have to prepare a quarterly P&L across the different funding pools.
It can be an interesting area to work in.