OPT can not go to a lower level, only to a higher level. So once you apply for an OPT for a Ph.D., you can never apply for an OPT for M.S. again. If you don't use up Ph.D. OPT, it's gone. For CPT though, you may specify the duration, such as 3 months, without using up all 12 months. Also, CPT less than 12 months, for instance, 11.5 months, won't disqualify your OPT. However, CPT of 12 months will disqualify your OPT altogether.