I can think of a couple of options. One would be to use Binary Stream's Multi Entity Management which allows you to assign transactions to an entity and then do check run's per entity (as well as pay on behalf of other entities).
Another option is Willoware has a set of tools called GP Powerpack and within that set of tools is one tool called Select Check Filters which would allow you to set up filters for selecting checks based on GL codes and segments (among many other filtering options).
I've used both in the past and both work well. MEM has alot of other nice functionality for keeping multiple companies within one database (i.e. automatic due to/from, separate 1099 printing per entity, security by entity, etc)
Here's a link to Binary Stream MEM: binarystream.com/.../multi-entity-management
Here's a link to Willoware's GP Powerpack: willoware.com/.../gp-powerpack