Ok so, I guess it depends on who your users generally are. Personally, I'd prefer if you provided an apt repo so I can install the software (and updates) that way, and use debconf to configure the stuff you cover in your 'setup wizard'.

On a slightly off topic note: I'm a little confused how your two apps work together/cross over? Or are they two distinct tools to do similar tasks?

Coincidentally story time: I am actually in the market for a replacement time tracking/invoicing solution (current solution is halting support of their self-hosted version in favour of their 'cloud' service). I think honestly the biggest issue for me is that I'm reluctant to make myself/my business so reliant on a proprietary system like that again. Unfortunately most open source tools in this space also have no, or terrible native client support (i.e. desktop/phone apps) so I'm kind of stuck right now.