The definition of stress is force per unit area. Area is measured in length x length. One of the "lengths" is in this case thickness. You use the corroded ( smaller ) thickness to calculate the stress ( which will come out higher than if you used the nominal thickness ) and compare that to the allowable stress.
Allowable stress is not ( usually ) calculated based on a material thickness, rather it is determined from the material properties modified by the design conditions ( temperature, risk, etc ).
I fear that by your questions, you may not be accustomed to using API 650 and given the risk to public safety if it fails due to a flawed design, you should consult an expert who is familiar with the code. Or at least have your design checked by one skilled in the art of such tank design.