Try using gimp or other software allowing you transparency in your graphics straight away would be best.
In Construct 2 you can paint or fill with "Alpha" set to 0 to get 100% transparency. See image below.
Note: You can have different Alpha-values allowing you not just a one-step (gif- or png8-) like transparency described, but really smooth anti-aliased edges to transparent areas are possible due to the png32-format. For that you will need to use software that can handle that properly.