You may or may not have seen the guide I have here ==>  http://line6.com/support/docs/DOC-2522

Probably the biggest single trick to getting a neutral patch is to get the levels right.  The most important one appears to be to boost the level before the Amp Input dramatically - 12dB - to compensate for a level drop at that point.   My recipe for a Neutral patch is as follows, from the guide ....

Patch Setup - Effects Only

This is a setup for a patch using Effects only.  The settings below are the same for both methods except those in red which are for the first method and blue which are for the second method:

Control

1. Start off by creating a completely ‘Blank’ patch with no effects set and no amp model selected.
2. Move the mixer device to the very end of the effects chain by moving all of the effects blocks in front of the amp model.
3. Add an ‘FX Loop’ effect to the effects chain somewhere near the middle.
4. Add a studio EQ just before the FX Block. No EQ changes should be set but the gain should be raised by +12dB *.  This compensates for a level drop between the HD Input and the HD FX Loop.
5. The mixer channel A level should be set to around -1.5 dB for method 1 or around -14 dB -12dB for method 2 and Panned to Centre. Mixer channel B level should be set to 'Mute'.  Note that this level may vary quite a bit between amps.  The best advice is to flip the Amp Loop on and off and adjust the Mixer output level until the level is the same with the loop on or off.
6. Any effects that you want ‘in front’ of the Amp can now be inserted into a free block to the left of the ‘FX Loop’ block in the effects chain. Typically these might include Compressor/Overdrive/Distortion and Wah.
7. Any effects that you want in the ‘Loop’ of the Amp can now be inserted into a free block to the right of the ‘FX Loop’ block in the effects chain. Typically these might include Delay/Modulation and Reverb.
8. Try and ensure that the ‘Output’ or ‘Level’ for each individual effect does not make the overall volume level louder or quieter.  This will avoid level problems with the patch overall.
9. Set ‘Input 2 Source’ to ‘Variax’ even if you do not have one.  This will reduce background noise on higher gain patches and will help keep the input gain at the right levels.   This setting is found within 'System Settings' but is set for each patch individually.

Do not select an amp model for an 'effects only' patch as this will then be in competition with your real pre-amp in and will probably sound poor..

*  Note (Oct 2012):  The FX Send level is set by the gain level Studio EQ in step 5 above and is dependent on your choice of Input sources.

• If you set your POD Input Sources to Input 1 = Guitar/Input 2 = Variax (as suggested in step 9) then you should set the level to +12dB as suggested.
• However, if you prefer to use set your POD Input Sources to Input 1 = Guitar/Input 2 = Same then you should set the level to just +6dB to avoid over-boosting your amp input and causing unwanted clipping.