Reordering scaffolds according to a reference without a genetic map
Have you tried Mauve alignment? Its pretty easy once you become familiar and has a GUI for further ease of use. Additionally there are a few online tutorials on how to re-order contigs/ scaffolds using this software. Heres one I use when in need.

Mauve contains a function called Mauve Contig Mover (MCM) which can be used to a) compare an assembly to a reference and/or b) rearrange contigs to improve assembly quality.   

I use the tutorial as above which uses the GUI for Mauve. I