Photoshop Layers / Smart Filters

Wondering if anyone can explain how to do this : a simple example. i have layer filled with color red.i turn it into a smart filter. i double click the smart filter. window opens up i see the layer filled with red. i fill with black, hit save. so far so good. problem is this. another example. i have bg layer filled with red and another layer. this other layer has small rectangle filled with black rotated with transparent pixels outside of it… if i convert to smart filter, double click it. i dont get nice neat rectangle to fill or what ever but the rotated rectangle with transparent pixels round it. so if i embeded anothe rimage on it. it would not take the rectangle shape but the whole layer. i want it to open up as the black rectangle only! not with transparent pixels. i know i havnt explained to good but maybe you understand what im trying to do.