Thanks for your questions.
1. You may hide the default check-in and check-out parameters from the front-end and email templates. Then add this information separately to the description of each accommodation type.
2. You may ask the guest to add a note about early check-in/late checkout in the Notes box of the checkout form. For this, you may edit the translation of the plugin to change ‘Notes’ label to something different e.g. ‘Let us know if you need an early check-in or late check-out.’