You really need to rename the files anyway because the count only goes to 9,999 and then returns to 1 again.
I have found the simplest way is also the most effective. I create a folder for each batch of photos. The folder gets a name with date and description like "2015-12-16; Suzy's birthday". Because each batch goes in its own folder it doesn't matter that they reset and repeat. When I process the raw files I export them as jpg files to a separate exports file with a similar name and I have Lightroom nalme the images themselves that way like 2015-12-16; Suzy birthday 1 of 16.