Tuning:  Hybrid
This section will help you tune to a hybrid between JUST INTONATION (abbreviated JI -- perfect to the ear) and EQUAL TEMPERAMENT (abbreviated ET - not the Extraterrestrial ).  The advantage of JI is that certain combinations of notes (like the tonic and 3rd of the root major chord) SOUND GOOD to your ear.  The disadvantage of JI is that, while the open chord sounds GREAT to your ear, there are many combinations of pedals and levers that do NOT.  For example, the E to F change on E9 ends up being more than 1/4 OF A FRET FLAT (that's WAAAAAAY FLAT).  The way I approach this is to compromise and arrive at a `happy medium' between `straight up' (ET) and `open chord perfect to the ear' (JI).  THIS IS HOW I TUNE.  THERE ARE MANY OTHER WAYS.  REMEMBER THAT PLAYING IN TUNE IS MORE IMPORTANT THAN HOW YOU TUNE THE GUITAR.

Will everything sound perfectly in tune open?  NO.  

Will common combinations require less `fudging' with the bar?  YES.

Does this have anything to do with PLAYING IN TUNE?  VERY LITTLE.
In practice, there are professional steel guitarists (Weldon Myrick, Buddy Emmons, and others) who tune pretty close to ET and there are others (Paul Franklin, Jeff Newman, and others) who tune pretty close to JI.

LETS CUT TO THE CHASE - STEP BY STEP

Prepare
Plug your guitar into your tuner
Push your A and B pedals and release a few times, then HOLD THEM IN

Tune the open E chord to compensate for detuning (cabinet drop, axle flex, etc.)
Tune the 4th, 8th, and 11th string E notes to be STRAIGHT UP (0 deflection) WITH THE A and B PEDALS ENGAGED
Release your A and B pedals
Check your E strings.  They should be 4-8 cents sharp (441-442 on the Hertz scale)
Tune the B's (5th, 9th, 12th strings) the same as the E's.  If the E's are 4 cents sharp, tune the B's 4 cents sharp
Tune the G#'s (3rd, 6th, 10th) 4 cents flat
Tune the F#'s (1st and 7th) straight up
Tune the 2nd string D# 4 cents flat

At this point all open strings are tuned
(a quick tutorial)
(how to tune pedal or knee lever pulls:)
(remember to engage and release the pedal or lever several times and then check the tuning of the open note without the pedal or lever change; bring the pulled note up to the desired pitch according to the tuner settings; engage and release several times; check the changed note; release and check the unchanged note; when they both read correctly on the tuner you're done with that change - REMEMBER -- the change should start out on the right tuner reading, pull to the right reading, and then return to where it started)

Tune the E9 A, B, and C pedals
Press the B pedal
Tune the A's (3rd, 6th, and 10th with the B pedal) straight up
Tune the C#'s (5th, 9th, 12th with the A pedal) 8 cents flat
Tune the C pedal E to F# on 4 straight up
Tune the C pedal B to C# 8 cents flat

I also use compensators on 1 and 7 -- both on the A pedal -- and tune them to match the C#'s

At this point the three E9 pedals are tuned
REMEMBER TO CHECK THE OPEN TUNING OFTEN DURING THIS PROCESS

Tune the E9 knee levers
On the lever that lowers 4 and 8 from E to D#, tune the D#'s 4 cents flat
On that lever, tune the 2nd string C# 8 cents flat

On the lever that raises 4, 8, and 11 from E to F, tune the F's 12 cents flat

On the lever that raises 1 from F# to G#, tune the G# 4 cents flat
On that lever, tune the 7th string raise from F# to G straight up

On the lever that lowers 5 from B to A#, tune the A# 8 cents flat

On the lever that lowers the 2nd string, tune the half stop D straight up
On that lever, tune the full stop C# 8 cents flat

At this point all knee levers are tuned

Tune the `Franklin pedal' (P4)
Tune the 5th string lowered from B to A straight up
Tune the 6th string lowered from G# to F# straight up

Tune the B6 pedals
P5:
Tune 12th string B to C# straight up
Tune 11th E to F and 7th F# to F 4 cents flat

P6:
Tune the 4th string E to match your open E (if it's 4 cents sharp, tune it 4 cents sharp)
Tune the 8th string D straight up

P7:
Tune the 5th string B to C# straight up
Tune the 6th string G# to A# straight up

P8:
Tune the 9th B to C 4 cents flat
Tune the 11th E to D# 4 cents flat
Tune the 12th B to G# 4 cents flat

Here's a chart:
ç
é
è
ç
è
F#
G#
0
-4
D#
D/C#
C#
-4
0/-8
-10
G#
A
-4
0
E
F#
E
F
D#
4
0
4
-12
-4
B
A#
C#
C#
A
C#
4
0
-8
-4
0
0
G#
A
F#
A#
-4
0
0
0
F#
G
F
0
0
-5
E
D
F
D#
4
0
-12
-4
B
C#
C
4
-8
-6
G#
A
-4
0
E
F
D#
F
4
-4
-4
-12
B
C#
G#
0
0
-4