I recommend adding your vote to the feature request for CIS if you haven’t done so already. We do actively monitor feature requests and investigate those with interest from the community (providing they are relevant to QuickFile and we have the available resources).
Tax reports will ignore the CIS payments, because we don’t directly support it, it’s just the workarounds that are available at the moment. However, we do have users (some with large accounts) using the CIS methods described in the knowledge base, without any issues.
The exporting of invoice lines relates to what I mentioned above:
While this isn’t possible at the moment, you’re welcome to start a feature request topic if you wish, requesting a file for the invoice lines. We can certainly consider this, especially if there are a considerable number of users looking for export.