You can only assemble scaffolds if there is sufficient mapping information (Genetic Maps, Optical mapping..). Many genome assemblies are only assembled to the scaffold level, so I think that in general (I don't know for your case) you can work with the scaffolds. The only think that you can do (since you have a closely related specie) is classify your scaffolds:
- Placed scaffolds: the scaffolds have been placed within a chromosome.
- Unlocalized scaffolds: although the chromosome within which the scaffold occurs is known, the scaffold's position or orientation is not known.
- Unplaced scaffolds: it is not known which chromosome the scaffold belongs to.
You can create AGP files (http://www.ncbi.nlm.nih.gov/projects/genome/assembly/agp/AGP_Specification.shtml) containing all the information about the relationship between contigs, scaffolds and chromosomes.
Hope it helps