Newbie project problems

I wouldn't say Simulink/DSP Builder is useless. You can use it to test out your design pretty easily. You can potentially do this: Simulink SINE wave block connect to a ADC block, which is connected to some sort of memory storage unit. Besides the SINE wave block, everything else can be built with Altera block. Once you have verified your design, you can program it onto the board.

Now to set the sampling rate... you can use the clock block. In the clock block, you can specify what the real world clock period is and also what each sample in Simulink signifies (i.e. each Simulink sample can correspond to 1 ms of real world clock or so). The combination of the two should allow you to create sine waves of different sampling frequency.

Also, you can always use the NCO core to create the sine wave of a specific sampling rate (as pointed out by mirimon).

Anyways, hope this helps.