A new company added by a partner can be included in their adviser list by logging directly in to that new company and entering the partner's company abbreviation into the Adviser field on the bottom left of the Company Settings screen (Setup > Company Settings). The next time the partner logs in to their partner account the new company will show in the list on their Adviser window.
When the customer is finishing their trial and continuing with FlexiTime, the partner can open the customer's FlexiTime company via their Adviser screen and select the appropriate package under Tools > My Account. Click Next, select Payment by Invoice, and then Submit.
The subscription will then be added to the partner's monthly invoice.