There are at least headings for FNA & marrows in the ACGME log system, so some people use it to keep everything in one place. Last time I was able to check, however, there was no heading for surgicals/cyto, etc., so it's just not possible to track via ACGME. Frankly it's easier to keep an excel or similar file and add your running totals there, then only transfer what you have to to ACGME -- but beware, as there may be items of information the log system asks for which you aren't keeping in your excel file.
As for surgicals, etc., myself and fellow residents estimated those as well, based on looking at several "typical" days on certain services and extrapolating.
Hopefully the autopsy service will once again become an active, involved educational experience for multiple specialties and medical students, rather than the "go do this because I don't want to and I don't get paid specifically for it" isolated pathology resident service. It seems to be one of the symptoms of the "business" of medicine. Meanwhile, IMO, if a program can't get its residents 50 autopsies in 4 years (or about 1 every month) it shouldn't bother having a residency program. Er, not that it technically -can- right now.