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For your question, please take a look my comments as below:
1) i disabled: BUCK_BOOST_EN_A, TYPE_A_VBUS_EN, PWM_A, PWM_A, PWM_OUT_A and Clock_3 in TopDesign TypeA. or should i removed it ?
>> Disable is enough for project customize. If you like 100% clean, you can remove it from TopDesign.
2) should i also disable in TypeC : PWMI_C, BUCK_BOOST_EN_C, DIR_CTRL_C and VBUS_CTRL_TIMER ? or remove it.
>> You should disable all of them.
>> Please do not remove VBUS_CTRL_TIMER if you would like to make the project is clean.
3) should i add pin 16 and 17 and as D- and D+ in the TopDesign and how ?
>> You do not need add pin assignment for pin#16 and pin#17 as for D- and D+, you just need make sure whether the BC1.2 and Apple Charging (If you want to support Apple Charging) have been enabled in the configuration or not.
The Configuration in Ez-PD configuration Utility
For Apple charging support and co-exist with BC1.2, you need external pull-up resistor on DP end, you can refer Cypress EZ-PD™ CCGx Power SDK User Guide, Doc. No. 002-22136 Rev. *A. Section 4.8 Legacy / proprietary charging configurations.