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