Mapping out a large house, with a lot of breakers, is a big task - no matter how you tackle it.
I suppose you could try and tackle it from the breaker end, or from the device end. Both will take lots of time, and a partner (and maybe a pair of cell phones of walkie-talkies) will help a lot.
Start with a drawing of the house, and mark each device location (switch, light, outlet, hard-wired appliance, etc).
Testing from the "breaker" end, you would turn off one breaker at a time, and then test to find what devices go out. Label those on the map, and then move on to each breaker, one at a time.
At the end, any un-marked devices on the map need to be re-tested, to figure out which breaker controls them.
Testing from the "device" end, you would go to one device at a time, and check to make sure it has power (a plug-in circuit test is handy for outlets). Have the assistant turn off one breaker at a time, until that device goes out. Mark it on the map, turn the breaker back on, and move on to the next device.
You could also do a combination (doing the first method for most of it, and the second method for any "mystery" devices).
Before doing the test, I would recommend unplugging anything that might be damaged (or annoyed) by repeatedly cutting the power (like computers, A/V equipment, HVAC - turn off the thermostat, and/or the shutoff switch on the unit, refrigerators, etc.
It will probably take at least a few hours to do, but you shouldn't have to do it again (unless you make major electrical changes without documenting them well).
Once you are doing that, I suggest marking which phase each breaker is on (most breaker boxes are split so that every other row (of two breakers) is on the same phase, while the alternates are on the other phase. Most breaker boxed are mounted vertically (with two vertical columns of breakers, and lots horizontal rows of two breakers each). Some breaker boxes are mounted horizontally, so the "columns" are actually the ones that alternate between the phases.
Even with a phase bridge/coupler/repeater, there is still potential for problems affecting one phase more than the other, so knowing how the phases are split in your house can help.
With two breaker panels, you might have additional issues. Depending on how they are wired (is one simple any extension of the other, or is it a separate feed from the transformer?), you may need a coupler/repeater/bridge in each one, and possibly connecting the two. There are other people here who would be better at answering that question than I am.