Once you have the FPGA programmed you can take it and put it in any PCB.
So what you need?...Power, clock, inputs and outputs....You do not need all
that the spartan board has, because that is a generic board. Maybe you will need
some signal conditioning but for now I do not think you should worry about that.
If in your example, a counter, you just need to know where the input is mapped
(you already must know since it wont compile if you do not say which are the inputs)
and the outputs. The example of a counter is a bad example because is ineffective,
i nother words, the fpga is big compared with the same circuit made using gates.
But is just an example.