This topic question might have been a better fit in the sounder/fish finder area, where SNIPS is our resident expert.
I will attempt to provide you some clarification and my random thoughts.
When you operate sounder in dual frequency mode; “usually”, our sounder will calculate the depth digital readout from high frequency (due to its high resolution properties). When the high frequency has lost its depth readout, the sounder will start using low frequency for the depth digital readout. If running a single freq, it will use that selected frequency to determine the depth number (unless using Accu-fish or BD).
Our sounders have two signal processing circuits. One is for processing of the depth digital readout and the other is for giving the echo image. The “Bottom Level” setting is for setting the threshold level, to detect bottom for the digital depth readout. The other sounder parameters, which relate to the echo image; such as “Gain” or “TVG” etc… are used only for the image of the echo picture. The default “Bottom Level” value for each Furuno model is different due to the difference of each bottom detecting algorithm. Depending on the selected transducer and mounting, you might have to adjust your bottom level adjustment from the default to establish a good digital depth reading. In general terms, the depth level shown (once detected) will be transducer depth and you should use the “Draft” setting to offset the depth, to compensate for your hull/mounting location. Once properly adjusted you should have depth within a tenth of a foot or meter (depending on your setting). Depth can be generally determined within a tenth of a foot due to the fact that sound travels at 1500 meter per second in salt water (1497m per sec in fresh water). As a basic rule (and disclaimer on my part), Fish finders should not be used for navigational depth. As it says in the book "Do not maneuver the vessel based on the depth indication alone. Grounding may result." This is mostly because once you get into the shallow waters with a sounder they begin to pick up bottom echoes, off the close in bottom. Digital sounders like yours are much better. Folks with analog sounders should go out of auto, into manual, and lower the gain, to help reduce the echoes and problems in shallow water. For analog sounders (normally) less than 10 feet will require manual operation and lower gain. Below 5 feet is tricky if not impossible, with an analog sounder (depending on many factors). The digital units are normally good to about 2 feet, even in auto.
More focused on your example; it sounds like you are picking up enough random clutter/fish on the high freq to keep it being used as your digital depth source. High frequencies provide the best resolution (due to the small wavelength) but it also has a weakness. High frequencies do not travel as deeply into the water as lower frequencies (because of wavelength). The fact that you are even randomly seeing bottom with your HF at 1000 ft, shows you have a very good install. If a target is between you and bottom, the digital depth can be affected especially if the bottom is not coming in good. I would suggest changing your HF bottom level adjustment where the HF threshold isn’t as easily exceeded. This will allow the sounder to switch over and start using your LF for digital depth sooner; as your HF becomes spotty.