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The normal way to do this is to paint on a layer above your original, you'd then have this layer set to whatever blend mode you need.

You say you use 'Rectangle' again...and yet up to that point haven't actually mentioned what that means or when or where you used whatever it is.

The 'Rectangular Marquee' tool is used to define an area for editing.

The 'Rectangle' tool is used to create a shape.

All shapes are created on their own layer.

If you could post a screen shot of your layers panel and a more precise description of your workflow and ultimate goal it would make it easier to suggest a solution for you.

Regards.

MrToM.