Depending on the nature of the project, I wouldn't waste your time with this tool in it's current condition. It will detect targets, and miss others. It will give you many more false hits than actual hits. The colors of the targets are not critical. They just need to be contrasted in the expected shape.
For example, on this project there were 3 actual markers. The tool was set to it's most restrictive tolorance and residual, (1,1), and the tool found 2 of the 3 targets and found 5 non-targets.
Maybe if the tool was shown an example of a target in the dialog box, then it could be more effective. Perhaps, if it was looking for blue pixels as in my targets, it could more easily eliminate outliers.