ASTAP ("Astrometric STAcking Program") is a FREE, competent, actively developed stacker, available for all platforms. Stacking and saving your data with these settings is essential to getting good results from StarTools.
Of particular importance is switching off "Auto levels" in the Stack method tab. Any sort of color calibration should be avoided. Once turned off, you will be able to import your ASTAP-exported dataset into StarTools with the second option.
Besides calibration and stacking, do not perform any further operations on the resulting dataset in ASTAP.
If stacking multiple mono datasets for use in a composite, make sure to use one set's finished stack as a reference to stack the others with; StarTools's Compose module requires every dataset to be the same dimensions. Aligning remaining channels against an initial channel during stacking is particularly important to ensure consistency of point spread functions across channels; do not align finished stacks against each other after stacking.
StarTools does more than just help you make "pretty pictures".
StarTools keeps a detailed log of what modules and parameters you used.
The Heal module was created to provide a means of substituting unwanted pixels in an neutral way.
You can convert everything you see to a format you find convenient. Give it a try!