When a new empty sequence is created, it is possible to set explicitely (from Local menu | Header) names of default program and method files, that will be assigned to each sample added to the sequence.
If no such file names are specified, added samples will have no method and program file names assigned. It can be assigned explicitely to each sample, or if left empty, the program or method from the sequence template will be used.
In the case, that a template file name (different from the sequence template) is assigned to the sample, than method and program from this template will be used for the sample processing (unless program or method file is explicitely specified for the sample, but it does not make much sense to assign a template and also both - method and program file names).