What version of Eagle do you use? I use Eagle 4.14 and do not know of a way to globally change all names to be, for example, consecutive numbers. That used to be a minor problem when I would "add" several common parts, like capacitors and resistors, to a work area, and then pull those parts into the schematic as needed. Now, I use the "delete and copy" sequence or "delete and add" sequence.
In other words, if you delete the part first, then add the new part using either the add or copy commands, the numbers will be sequential. Of course, they may not follow a logical sequence across the schematic, but that might be asking too much for the program to do.
John