If you have more than one indicator on a chart that colors the bars, you may find that they're competing with each other, and you can only use one bar-coloring indicator at a time. But there's a way to show more than one bar-coloring indicator at a time. So yes, you could have MQ Trender Pro 2.0 settings the colors on the top part of the chart, and ValueBars appearing in the panel below it, with the bars aligned between the two.
To do so, you must add a 2nd Data Series to the chart. Open DataSeries, add a new data series with the same settings as the first data series added to the chart. This will cause the price data to appear twice on the chart. Assuming this is the first thing being changed on the chart, you'll then have the same DataSeries on Panel 1 and Panel 2. ValueBars works best with OHLC bars, so you can change the chart's ChartStyle setting to OHLC, or to whatever bar type is appropriate for the indicator you plan to use on it. In the following image, the 2nd DataSeries is set to OHLC:
Now with a 2nd OHLC DataSeries added, we can overlay ValueBars on top of it. To have ValueBars appear on the lower DataSeries you added, make sure the indicator's Panel input is set to the same panel as the 2nd DataSeries, e.g., panel 2. Your indicator settings may appear as follows, with 2 entered for the Panel input:
You should now have ValueBars on the lower panel, separate from the initial price data above it. You can have other indicators added to either or both panels, and you can add indicators that appear on the panels below the two data series. Here's an example of a chart with MQ Trender Pro 2.0 on the top data series, ValueBars on the 2nd data series, and MQ Momentum underneath. If you see interference with your indicator and the display of the data bars, you can make the chart bars transparent by setting both the up and down bar colors to Transparent in the DataSeries that's interfering with it.