Thanks for your quick answer!
I thought about using a daughter card, but there are a few reasons why I don’t want to do it right now. The company I work for produces embedded devices of certain size and shapes; I want to make a board of the same size.
An other reason is that one of the application I'm going to implement is going to take roughly 15 000 LEs. I made a rough estimation, it is right now in Simulink and I used DSP builder to make this estimation. Knowing there might be other things running (NIOS 2, PC104 interface ect) 25 000 like on this board might be a little short. So this is why I’m going for the EP3C40.
Now what I'm doing is research and sees if this is possible. If the board I'm planning to make does not work, I’ll probably go for the daughter card.