To use my fonts commercially, I request a payment. For most fonts, this is $10 USD.
The easiest payment for for me to accept is via paypal, to email@example.com.
If you wish, I can invoice you for that amount, so you will have a record of the transaction.
Normal commercial licensing would cover use on up to 5 computers.
A logo is higher profile use, and I generally negotiate that proportional to the size of the project.
I don't want to be unreasonable and take advantage of small companies, but I do want to be compensated for high profile use. A corner grocery store would pay less to use a font for a logo than a blockbuster movie would.
Each logo application is different, and negotiated seperately. As a guideline, I propose 0.1% of the project or annual budget, or the single license fee, whichever is greater.
If it is a $10,000 project, it would cost you $100 to use the font for the logo.
If it is a Million dollar project, it would cost you $1,000 to use the font for the logo.
Preferred payment is via Paypal.
Actual fee settlements have ranged from double the normal license fee, to several thousand dollars for exclusive TV in perpetuity rights for one particular font.