SQL Server and SQL anywhere compatbility
There's no reason why you should have a problem running SQL Anywhere and SQL Server on the same machine - so long as you have the appropriate resources to meet the needs of both. That will depend entirely on how busy the various databases are. We have many machines running both. 

NB There is no connection between the code bases of SQL Anywhere and SQL Server. SQL Anywhere is a development of WATCOM SQL and although it was owned by Sybase and now SAP, it is an entirely separate product from Sybase (now SAP) ASE - Adaptive Server Enterprise, which did originally have a common origin with MS SQL Server.  

If you run into any problems it might be worth posting on http://sqlanywhere-forum.sap.com/questions/ which is a specialist SQL Anywhere forum.