My limited experience with this problem is the same as Preston's. Follow his advice in using the TimeTracker, but be especially reluctant to ever add manual hours in your work on an Upwork project.
A client never has any obligation whatsoever to ever pay you for manual hours you book, even if the client specifically agrees that you are "allowed" to add manual hours. (This has nothing to do with whether or not the client has a problem with his/her payment method. That is a completely different situation, though I'd expect Upwork will not pay you for any manual time on a contract when the client can't pay Upwork for any work time you've legitimately booked.)
If Upwork has to pay you when they are not being paid by the client, that is Upwork's "hour paid for an hour worked" guaranty to freelancers. It's probably one of the most important features of Upwork for at least some freelancers.
However, it is my experience Upwork will then go through your TimeTracker records to closely review all hours you have booked throughout the life of the project. This is where it will be vital that your memo for each time you use TimeTracker be clearly written so someone other than your client can understand it. For example, your memo might say something like, "Phone call re calc. def.", which your client Fred might have no problem understanding and would not contest when reviewing your TimeTracker records. But an Upwork investigator who knows little about your project might say tht wording does not create a sufficient explanation of the work you were doing at that time.
In that case, Upwork can disallow the time you booked using TimeTracker. You will not be told what has caused Upwork to make this decision nor can you object to it. Upwork will return to itself the payment you received for that work time and you will have no recourse to recoup that lost income.
Clear memos are indispensable to assuring full payment under hourly projects.
