Now, when using flash, I set the camera with manual settings to suit the scene and let the flash find its own self adjusted level; with a bit of flash output compensation when required. This does initially take a bit of experimentation before you get the hang of it; but this will allow you to be fully in charge of your settings and enable the best results. This could have enabled you to shoot with a narrower aperture for better focus depth.
Flash rebound or hotspots etc can be difficult to avoid though, even with careful camera adjustment. Being square to a subject is often problematic which is why many flash photographers mount their flash away from the camera, or try a variety of other special tricks. However, this soon gets rather complicated with studio photography jargon and special equipment.