I would strongly suggest using BRIG (Blast Ring Image Generator) instead of Circos. It gives slightly more granular images in my opinion, with much less messing about.

You can use this tool which is based on CIRCOS, but easier to use if you are not very proficient with coding stuff: http://omgenomics.com/circa/

You might consider investigating if a hive plot would give you a less convoluted figure.