Hello Viking69,
PhotoScan Standard has no referencing instruments, so the default model orientation in space is arbitrary. However, you can rotate the model relatively to the coordinate system axis using Rotate Object tool.
Texture atlas may consist of big number of charts, if you are using Generic mapping mode. Only Orthophoto mapping mode produces single chart atlas. Also you can create a custom UV in the external application based on the exported model and then import it back to PhotoScan for texturing.