Inside a flat there is no Pishach bhoomi dosh and no need to leave corners or sides empty; that space can be used. Devta marking is still done in the usual way, for example to judge the main door location.
The flat is the area you can enter and use; a portion cut off by stairs, a lift or a neighbouring flat counts as a cut. A flat with cut corners, such as a cut South-West and North-East, is marked the usual way: take the centre and north, place the chakra and mark the devtas, drawing lines from the centre to every corner to set the bands.