Sadly there is no way to have footprints aligned the same way as in the schematic. (With inbuilt KiCad functionalities)
For most designs it would not make much sense anyways as the schematic is not really intended to represent the physical layout but an abstract view of the function of your system. (The same physical component can be spread out over a number of sheets for example.)
KiCad does however group footprints by hierarchical sheet. If you use a well made hierarchical design then this should already be enough to find things that belong together. (plus the select from same sheet tool found in the right click context menu will add another option to work with such a design.)
There might however be scripts available. So with a bit of luck somebody knows something.
Also very useful is the fact that kicad will highlight the footprint if you click on its symbol. Meaning if you have layout and schematic open side by side you can easily select a specific footprint by clicking on its schematic symbol.
EDIT: Sorry, the thread is about something else… I’m too tired…
For “geographical annotation” see RenumKiCad PCB Update. IIRC @DocumentedDesigns has contacted the dev mailing list and wanted to get it to KiCad proper. I don’t know about the current state.
As I managed to teach myself the relevant development packages I am working to incorporate geographic backannotation into Kicad. I am hopeful this can be done for V6.