There seems to be some confusion here. Your example looks like it is the filenames you are changing. Filenames and titles are two completely different things.
Most ereaders will use the books true title, a field in the file's metadata, when listing the book. They generally fall back to using the filename only when the book lacks a true embedded title. Changing the filename will not change the display when there is an embedded title.
The best practice, IMO, is to keep the Title file unaltered and to use the Series field for ordering a series (e.g. "Alex Cross [01]"). In your example, the Title would be "Along Came a Spider", the Author would be "James Patterson", the Series would be "Alex Cross", and the Series_Index would be "1" in calibre. Then:
- alter the save template in Preferences Save to Disk or Send to Device (or both) to do the filename modification automatically
- add a Metadata Plugboard to alter the true embedded title.
This way, calibre will do the modifications for you automatically when you either Save to Disk or Send to Device.
I use a save template like "{series} {series_index:0>2s} {title} - {authors}" to get filenames similar to your example. My plugboards (one for each format that I use) have "{series} {series_index:0>2s} {title}" as the source with "title" as the destination and "{author_sort}" paired with "authors", which alters the embedded title in a similar manner.