If the AHRC receives more than one funding nomination on your behalf (e.g. from 2 different universities), they reserve the right to exclude you from the competition, I think. Technically you are only supposed to apply for AHRC funding at one institution, but I believe quite a few institutions are tacitly ignoring this.
The best way to proceed, if you insist on applying for funding at 2 institutions, is to wait for the outcomes of your applications (normally they will interview you before nominating you), then, if one is successful, inform the other institution that you are withdrawing from their competition... if that makes sense. Basically, make sure that you don't have 2 different institutions submitting you to the AHRC at once, or you're in trouble!