Hi, I'm trying to speedrun Poochy and Yoshi's Woolly World on Citra, is there any way to begin timing it exactly when I gain control? If not, what happens if I begin or end timing too early or late?

I'm unfamiliar with making autosplitters, but you shouldn't need to worry about timing, other runners use a manual timer like LiveSplit for their runs. Even if you accidentally start your timer at the wrong place, you can always retime the run based off the video. Having a visible timer is usually just for convenience.