Consultation and design fees can be difficult to calculate and ask for, but you are trying to make a living. When you call your accountant or lawyer for advice the clock starts ticking as soon as they start listening. You should not be a whole lot different.
Establish at the beginning that the project includes a specified number of hours of planning/survey/meetings, of agency management, and of creative work. Other things may be added as the project requires. Also establish that exceeding those hours by 10% (or 5% if it’s really big) will incur additional charges.
Once into the project give weekly updates on how much time has been used and the progress achieved. That way, if the client starts adding things or changing their minds, they understand the consequences. If they think it’s worth paying for, great. If not, take it off the table. You can always be generous and waive the extra fees, but giving clients that kind of choice saves a lot of resentment (and time) on both sides.