If you don't have a good supervisor structure in place before you start your project, that needs to be your team's top priority. This is especially true if you are using a time keeping system because they will rely heavily on your supervisor structure for time approvals. The same thing with your position structure. If you currently don't have a strong position structure, start thinking about how you want to restructure it - if you don't, it will have a negative impact on your time keeping, regardless if you're moving to a new system or changing it altogether.
This is also a great time to decide what level of detail you want to default into your system. What do you want the timekeeping system to manage? For example, if you don't want the accounting unit to create a position for every single one that might be hit by your timekeeper, then maybe that's best left to your time entry system. These decisions should always be made ahead of the project so that you're not going back and restructuring your positions when you do your project, which runs the risk of negatively impacting your payroll processes.
On our first payroll project, we rebuilt ours twice and continued modifying them right up until go-live. This was a net new implementation, which is also another reason to get a handle on that right now if you're thinking about moving payroll systems. The best way to get ahead of this is by identifying leads that have functional experience in HR benefits and payroll and moving them on to this project, if they have the capacity.