Usually I delete parts of an image (Extra parts, or stuff that needs to be clear) from a image editor on my computer, then I upload them for use, now those deleted parts show up as white in Scratch, and the only way to actually delete parts is from the Scratch editor, which I don't really like to use…
This used to work in the past, why isn't it working now? I can provide more details if needed.

Could I ask what image format you're saving to before uploading? Some formats, like jpg, don't have the alpha layer that allows you to make images transparent.

I use .png to save my images, as that worked before.