Have had a couple of technical issues, and website directions can be misleading or just too vague for people unfamiliar with the system or with running payroll. I'm with a tiny nonprofit organization, and was hired as sort of the part-time "all in one" admin person, with payroll being one of the responsibilities. I have no prior experience with payroll.
It's basically straighforward, but when you have a unique situation, I have found the infomation/instructions on the website to be vague and often misleading. Example: "a paper check will be issued" should probably say "employer will issue a paper check to employee" - the way they word it definitely leaves open the understanding that Zenefits is sending the check. (Perhaps they should contract with a technical writer for this - couldn't hurt.)
I had a similar issue with Contractors module. Needed to issue a Form 1099 for someone. When you check the "yes" box to have Zenefits issue it, they ask you "How much to you want to put on on the 1099"? or something very similar. Being new to this, I put in the amount of money the contractor had been paid based on Zenefits' payment history.
Contractor got a 1099 for double the wages she actually earned. Turns out what they MEANT was, "Zenefits shows total payments of $$$. Do you wish to add additional payments to the 1099"? Luckily, I had some IRS form and I could issue the corrected 1099 because Zenefits could not. Had I not had the forms their only suggestion was to pay a CPA to issue the correction. They should just be more precise in their language.
The Time and Attendance thing seems a little buggy - recently I had to add hours to some employee's timecards after the deadline, and hours I added to one employee's card ended up also in another employee's card (employee 2) - and the hours that employee 2 had added to their card had disappeared. I did not see that because I had not edited employee 2's card. Result was employee 2 was overpaid. Did not get a response as to how to fix this before the next pay run, which is annoying. I also log my hours on a spreadsheet as I work, then transfer them to Time and Attendance. I can never get my hours/minutes/totals to work properly in T&A. I have to tweak the decimals in T&A to make the total hours match what I show in Google Sheets.
Watch for bugginess and before you do something new, make sure you either watch the tutorial or ask Support to be sure you are doing it right. The website directions make it seem that you understand what you are about to do, but the wording is poor and it's easy to make a mistake.
The payroll account was in place when I started, so no idea what problems might be solved. I added Timd and Attendance because it was too time-consuming to do manual timecards and ensure compliance with the overtime laws, etc. It is faster but as I mentioned above, it's buggy.