Hello Thomas,
PhotoScan does not support aligning functionality for the imported models using markers (markers could be placed on the model only if they are seen from at least two cameras).
But you can merge PhotoScan model in one chunk with the imported model in another chunk if chunks are in one coordinate system. PhotoScan model in the first chunk could be referenced to the imported model corresponding coordinate system (even local) using markers. After the first chunk is referenced by markers it could be merged with the imported model's chunk.