I think that the number in front of the file name in the template tree simply defines the order in which the files are processed. IIRC I've had to check out the order of processing in the past if ever I wanted to get anything inserted in a generated file in a particular place. You have to figure out what order the particular template directories are processed in too! I think the expand-template process starts with /templates and builds a list of things to do and then modifies this list by looking in /templates-custom before going ahead and doing the expansion.
Perhaps its just due to my not understanding accounting, but does any one else find SQL-Ledger to be temperamental and illogical?