There is some degree of spatial information within DNA. There is something called “hox genes” which are arranged on chromosomes in the same order our body parts are arranged (head, neck, thorax, hips, legs, in that order). There have been experiments where fruit flies genomes were edited. Basically the hox genes positions were changed and the flies has feet instead of antenna on their heads.

More precise spatial information such as having 5 fingers that are on the end of your arm is given by cell signaling mostly. During the development of an embryo most things are related to cells releasing certain molecules that cause other cells to move or differentiate. But the actual code for all those things is in our DNA as well. However the exact processes are still being researched and it’s not 100% clear how it works.

Edit: just a thought that occurred to me: I think if we knew the exact mechanisms of how this works, medical science would be creating functioning 3D organs or something close to that