long story short, I use the following as /usr/bin/wine-auto:

#!/usr/bin/env bash
x64=`file $1 | grep "x86-64" | wc -l`
if [ $x64 == 0 ]; then
   export WINEPREFIX=$HOME/.wine32
   exec wine32 "$@"
else
   export WINEPREFIX=$HOME/.wine64
   exec wine64 "$@"
fi


it assumes that 64bit wine is in ~/.wine64 and 32bit wine is in ~/.wine32

-- 
Marius
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