Hi Glen,
Welcome to 12Pay. It's very easy to learn and I've found the staff very helpful.
On your questions, (and this may not be the "official" way to do it, but it's what I've discovered during my use of the software):
1. Once you've set up your employees, you can click on each one, go to the 'Personal' tab, where you enter address details, etc. and alongside 'Home Phone' you'll find an employee number. I've tried changing this and it seems to work. Interestingly, if you add a new employee and the number exists, it adds an 'A' after the default number, but you cannot change to a number that already exists. Therefore, you may need to work backwards from the last employee when re-numbering.
2. Again, on the 'Personal' tab, you can find a drop-down menu for department. Initially, this is empty. However, once you enter a department, it becomes available on the drop-down menu for every employee and you only have to click the right one.
3. Under the Company Name, you will find the label 'Payments/Deductions.' Click the '+' at the side of this and there is a menu of all the possible payment types. The first option is to add a payment type. Therefore, you can either use one of the existing payments, or, if none of them are suitable, you can create your own. There are tick boxes on the payment and deuction definition pages that allow to specify if it is to be added or deducted with or without tax and NI being taken into account. You may need to play around with these to get it right.
4. When you click the button at the bottom of the 'Payroll' screen to advance to the next period, the software automatically generates a pop-up P32 showing the whole year to date. Be careful with this, however, if you have more than one payroll, such as a weekly one and a monthly one. The P32 will pop up when you finish the first payroll, and again when you finish each of the others. The safest way, in this case, is to ignore all the pop up P32's and follow the alternative steps below.
4 - Alternatively, when you click on the company name at the top of the left-hand window, you will see 'Reports' at the bottom of the right-hand window. Click this and two of the options are 'P32 (Payment Detail)' and 'P32 (Payment Summary)'. The titles speak for themselves, but the answer is the same. On the right hand side of the report is a column showing the totals for the month/quarter/year.
4 - Continued - The summary report also has a 'Pay HMRC' column on the left hand side. I don't use it, but on the 'Payments' tab in Employer Maintenance there is a button to record payments you have made. If you keep this up to date, then the P32 reports will take this into account when showing you how much to pay.
Hope this helps. There may be more information that the support desk can offer, but this should get you to a position where you can experiment.
Regards,
Michael