to get multi-uv tiles to display correctly you need to use polygroups. With your subtool selected go to polygroups>UV groups. This will display polygroups based on your UV tiles. Now ctrl+Shift each polygroup to hide/show and import your textures and apply as normal.
Now you can use the usual method of texture to polypaint and continue texturing.
Or if you’re painting in Zb and not importing existing textures then just paint your textures and use the multi-map exporter to export your maps. This will export multiple files depending on how many UV tiles you have set up. ZB will save them and include: u0,v0-u1,v0…etc. in the file name.