Programming Problem

if u are talking about the unused pins,in quartus gpi,u can go to settings->device&pin options->unused pins and select the state of unassigned pins there but if u are talking about the assigned pins,u should check your vhdl code of those pins' corresponding component and see and set the initial state of those registers.If the initial states are logical low and after programming u see those being high,this means the fpga isn't programmed normally and u should check the component's editor tab in sopc builder by right clicking the component and clicking edit comp.