There is no flat as such with a filter preamp the filters are engaged all the time. (Unless you have the ACG DFM which has an active/passive option) This is a common misunderstanding made by people who don't really understand how they work. There is however a close to flat as you can get setting.
Stack 1 is the volume/blend.
Stack 2 Upper ring fully of. Lower ring full on. This is the filter fully open so the full range allowable by the filter is allowed through.
Stack 3 as stack 1
Stack 4. Upper ring fully of. This is a gain so with it fully off the highness filter does nothing so the lower rings position does not matter.
Both pickups are now useable with the blend and both filters are open the highpass disengaged.
The way I would go from there is to move the blend on to the bridge pickup. Then adjust the lower ring of stack 3 until you get something you like. I generally close the filter to a degree to cut the top end so I have a more mid heavy sound.
Now move the blend to the neck pickup and do the same. I would normally generate the bottom end from there which again means closing the filter to remove the top end and some of the mids.
So you have reduced the preamp to a Volume/Blend/Tone/Tone and that is basically all it is.
Now use the blend to go between the two pickups to change the overall sound.
The upper ring on stack 2 and 3 just boost the effect of the filter cut off so you get more filter effect if you turn them up. I like them in the centre detent.
The preamp only appears complicated if you try to adjust every thing at the same time if you take it one thing at a time it is not that complicated but it does not work the way a 3 band does and most people approach it that way and generally can't get what they want. This is a common problem and it is why filter pre-amps are not that common people as a rule don't really get them. For those that get their head round it you will get sounds you will struggle to get with any other on board pre-amp. But there is a learning curve and some people just don't get on with them which is why I have always offered an alternative to the filter preamps.
If you don't get on with the pre-amp and like the bass just replace the pre-amp would be my advice. Sell an 01 will not be difficult and the East Uni-Pre will fit the cavity it is what I use for builds that don't need the filters.