They are going to try to indict Manafort on some stupid financial charge.
All prosecutors start by indicting minor figures for minor crimes, and then trying to get them to testify against higher-ups in exchange for leniency.
Mueller can easily get an indictment of Flynn for lying on his security-clearance application and can probably find something to hang on Manafort too. The question then becomes whether either of them flips, and on whom.