I see that your CA notary manual on page 9 says you must record the fee for each notarial act, in each journal entry.
The first thing to consider is whether you must keep track of your notary fees for tax purposes. If you want to, you can exclude them from your income for social security purposes, up to the amount you receive for the signing. (They are still income for income tax purposes.) But if you do this, you may reduce your retirement income, and reduce your disability income if you become disabled). Talk to a tax professional.
If you do need to keep track of notary fees, set the fee per entry to the maximum allowed, if this adds up to less than the total you're getting for the assignment. Otherwise, divide the fees up evenly among the notarizations so they add up to the total fee you're getting.
If you don't need to keep track, you could create a fee policy in your business records, saying that you don't charge any notarization fees for real estate signings, but do charge a fee for printing/travel/scanning/waiting/etc. Then record your notarization fees for these appointments as 0.
You'll always want to calculate your notary fees for general notary work. For these, the only fees will probably be travel and notarizing; if you called it all a travel fee, that might appear unreasonable.