There are two possible approaches.
1) Task approach - Processor Expert is generally task-orinted so unless it's really necessary you should not ask "how to connect two timers", but the questions should be "how to produce 1ms periodic interrupt" or "how to ouptut PWM pulses on a specific pin with given period etc..". This way you can use beans like TimerInt, PPG, FreeCntr etc... that allow to use chained timers for achieving long times. PE generates initialization code and runtime methods for you.
2) Peripheral approach - If it's necessary or you really want to handle low-level peripheral configuration including advanced fuatures, you can use peripheral init beans.They are peripheral specific. In your case, you can add three Init_TMR beans into the project (one for each timer) and configure their properties (Primary and secondary clock source, operation mode etc.)
best regards
Petr Hradsky
Processor Expert Support Team