If the control system seems good, the auditor will spend a lot of time testing its effectiveness and this gives the auditor evidence that the FS are probably free from material misstatement.
There will in addition always be some substantive testing but this will be much more extensive to the internal control system is poor. Internal control is poor the only way that the auditor can try to eliminate the presence of material misstatements is to look directly at the figures in the FS and gain evidence about those.