I hope that Andy or Jeremy will jump in correct me where I might be wrong in this post. I am still learning so forgive me if I misinformed on any of this.
There are a couple of things that are to be done to make sure your machine is running at its optimum. As XPMan indicated, when you start you machine the coil should be in the air and never on the ground because the ground reading will severely impact the performance of the machine. Improper ground balancing will affect the performance of the machine drastically. If you're running in Manual makes sure you periodically look at the screen to make sure your setting and what the machine is sensing are not too far apart from each other. Setting the level slightly lower than what the machine senses will gain you some depth (in "cleaner" soil - without magnet minerals) Manual and Pumping allow for the best performance.
You should set your Reactivity first and then go into the Reactivity Expert menu and set the Silencer Level you desire. If you change Reactivity during your hunt, this will also change your Silencer setting. You will have to go back into Silencer and readjust it to the desired setting. The lower the Silencer, the faster and deeper the machine will detect. It can make the machine more noisy though. Lower Reactivity with increase depth in "clean areas". Higher Silencer will quiet the machine down but sacrifice depth.
Lower Audio Responses will make it tougher to hear the deeper targets but if you raise this adjustment too much all depths of targets will have the same volume. I like to run at 3 or 4 so I can tell difference between a deep and shallow target without having to look at the screen.
If you have setup Notches and change Frequencies, you will have adjust your notches again so that you aren't "ignoring" targets that will now appear at a different point along the TID "line". Notching, instead of Higher Discrimination settings will not sacrifice depth.
Depth is also impacted by some other settings: Sensitivity being a BIG one. The higher your Sensitivity, the deeper detection depth but this will also make the machine more unstable. Under the Sensitivity Expert menu, is TX Power. This increases or decrease the "Transmit Power of the coil, but drains the coil battery faster and make the machine more unstable. Lower frequencies will get you depth. However, 4kHz loves iron. I do like 4kHz, but have been leaning toward 8kHz recently.