3-series processors have a 'ready' signal you can use to drive your startup sequence on the one of the hardware slots..."programXX_start_f"

A basic program probably doesn't need much initialization, maybe some serial and analog values. All depends on what you're trying to do, but unless you're reading in config files from NVRAM etc, you aren't likely to overload the controller on a 3-series anyway.

On 2-series, I usually used the '*out' on an srlatch to start a stepper to space out the initialization process.