How to plot two axis bar chart side by side

Update: An alternative approach with a minor modification of the code in OP:

1. Reverse the columns in q1: i.e. use q1 = qq[[All, {2, 1}]];, and
2. Use BarSpacing -> {0, 1} in both charts

q1 = qq[[All, {2, 1}]]; q2 = qq[[All, {1, 3}]];
qw1 = BarChart[q1, BarSpacing -> {0, 1}, Frame -> {Left}, 
      ChartStyle -> Darker[Red], FrameStyle -> Darker[Red], 
      ImagePadding -> 30, ImageSize -> 500, ImageMargins -> 4];
qw2 = BarChart[q2, BarSpacing -> {0, 1}, Frame -> {Right}, 
      FrameTicks -> All, ChartStyle -> Darker[Blue], 
      FrameStyle -> Darker[Blue], ImageMargins -> 4, 
   ImagePadding -> 30, 
      ImageSize -> 500];

Overlay[{qw1, qw2}]

Use BarSpacing -> {-.5, 1} in both charts to get:

Original answer:

You can use the function modifiedrange from this answer to rescale the second data set and use Charting`FindTicks to relabel the ticks on the right frame:

ClearAll[modifiedrange]
modifiedrange[{{a_, b_}, {c_, d_}}, z_: 0] /; z <= d := {(a d - (a - b + d) z)/(b - z), d}


{data1, data2} = Transpose[qq[[All, {2, 3}]]] ;
data2b = Rescale[data2, modifiedrange[MinMax /@ {data1, data2}], MinMax @ data1];

tickF = Charting`FindTicks[MinMax@data1, modifiedrange[MinMax /@ {data1, data2}]];

BarChart[Transpose[{data1, data2b}], 
   ChartStyle -> (Darker /@ {Red, Blue}), 
   BarSpacing -> {0, 1},
   ImageSize -> 500,
   Axes -> {True, False},
   Frame -> {Left, Right}, 
   FrameStyle -> { Darker /@ {Red, Blue}, {Automatic, Automatic}}, 
   FrameTicks -> {{Automatic, tickF}, {Automatic, Automatic}}]

Use BarSpacing -> {-.5, 1} to get

You can use ChartElementFunction to manually nudge the bars over by a bit, the following for example moves them 0.5 to the right:

ChartElementFunction -> (Rectangle @@ Transpose[# + {0.5, 0}] &)

For the combining part, you can search this site for ways to overlay charts cleanly (e.g. this question). One way is to use the CombinePlots function from the ForScience`¹ paclet:

<<ForScience`
qq = {{a, .261, 93}, {b, .247, 136}, {c, .311, 70}, {d, .336, 
    80}, {e, .339, 71}, {f, .337, 60}};
q1 = qq[[All, {1, 2}]]; q2 = qq[[All, {1, 3}]]
qw1 = BarChart[
  q1,
  BarSpacing -> {0, 1},
  Frame -> Left,
  ChartStyle -> Darker[Red],
  FrameStyle -> Darker[Red],
  ImagePadding -> 30,
  ImageSize -> 500,
  ImageMargins -> 4
  ]
qw2 = BarChart[
  q2,
  BarSpacing -> {0, 1},
  Frame -> Left,
  ChartStyle -> Darker[Blue],
  FrameStyle -> Darker[Blue],
  ImageMargins -> 4,
  ImagePadding -> 30,
  ImageSize -> 500,
  ChartElementFunction -> (Rectangle @@ Transpose[# + {0.5, 0}] &)
  ]
CombinePlots[
 qw1, qw2,
 "AxesSides" -> "TwoY", (* move the second plot to the right axis *)
 PlotRange -> All, (* ensure that all the bars are shown *)
 Frame -> {Left, Right}
 ]

¹You can install the current version using

PacletInstall["https://github.com/MMA-ForScience/ForScience/releases/download/v0.88.45/ForScience-0.88.45.paclet"]