When using twEERcer and BE I am only supposed to use one setting correct (ie: position 3)? Or do I need to write the same tune to the different positions?

Finally Should I have cleared all of the previous twEECer tunes before loading my BE tune?

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You can write a different tune to all 4 positions. Make sure you have TwEECer enabled in the hardware tab.

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1990 Mark VII Twin T3's JYTT--60# --stock block 306, HCI--AOD 3400stall--A3M1--Moates QH -- BE/EA
1989 Mark VII S/C 6 speed. HCI--42#--Vortech--Anderson B31--LT's--All the goodies--QH -- BE/EA
1987 Buick GN 61mm, ported heads/intake, other stuff...`
2002 Lightning -- Whipple @24#, 60s, LTs, SBTB, 3400stall, Everything Else....