I recieved Unemployment form Minnesota, this included payment from minnesota and the federal unemployment bonus. Does it all get allocated to minnesota?

Please clarify what you mean by allocate- if you were a resident of Minnesota all year you do not allocate your income. You would report all income unless subtracted or exempted by state law.  Unfortunately, you are being taxed at the federal and state level. 

I'm legally a SD resident, but I am a student and I work in Minnesota, The unemployement was for my job in Minnesota. That's why it's asking for allocation and since not all of the unemployment money came from the state of minnesota I wasn't sure if it qualified to be taxed in minnesota.

In a multi-state unemployment claim, the state you currently live in is the agent state. The agent state is the one that manages your unemployment claim. You apply to that state for benefits, explaining that your 15 to 18 months of previous wages were in other states. Once the agent state hears back from those states, verifying your eligibility and compensation amounts, it distributes your payments. Therefore, what ever State actually "covered" this unemployment that was paid out to you is the State that you should have - or should be - received/receiving a 1099-G Unemployment Statement from. You would not pay taxes to more than one State for unemployment.

You allocate all the unemployment  to SD, you home state, even if the compensation was paid by MN.  It's works this way in most (if not all) states.