Open eCabinets, but do not load a job or cabinet. From the main opened screen of eCabinets click the CNC button. Choose your jobs, change material properties if needed, filter parts out if needed, and pick the output location for the .twd file.
You may have specific reasons to "combine" the layout jobs within eCabinet Systems itself, but if you are only looking to have the "jobs" optimized/nested and cut in one run, you can simply create a TWD for each "layout" job in eCabinet Systems. Then, in Control Nesting, [LOAD] the first TWD then [ADD] the second TWD and [Nest] and [Write CNC] for the combined jobs.
Unfortunately, I have not dealt with the "Shopbot Link", but the documentation appears to indicate that there is both a [Load] and an [Add] option for TWD files.