You are here in the PRoC furum. A PRoC can only perform what you want using two TCPWM components.
In the PSoC 42xx BLE world there are UDB - based components which you may use for your purpose quite better. There you find flip-flops and look-up-tables that will help you generating the two desired waveforms with the appropriate frequency.
A timer isr would be the easiest solution and will probably work up to 1kHz but might get distorted by the BLE interrupts.