There are 2 types of SEO work.
1. Building the site to make the most out of search engines.
You covered this above, and yes it is mostly a one off job with a one off charge. You can also make sure you are making the most of things like Google Maps and Google Shopping if applicable. Also worth looking at making search engine sitemaps, by generating XML feeds.
I include this in all work I do as I take pride in the sites I create, if my client's site is successful, then I will do well too. In my mind this is what really works to improve results, and keeps on working for you for the life of the site. You could spend a million quid on PPC campaigns, and if you have a shit site, you will struggle to convert these visits into sales, and as soon as the campaign is over, your natural search results will suffer as you fade away into page 2.
2. Managing Advertising campaigns, such as PPC (or PPA).
This requires research of the current company to find the keywords most likely to be used for people trying to find the website, and researching competitors too. This side of things is where the money in SEO really is. Anyone who knows how to operate a web browser, that has a bit of common sense, can do this.
Usually what happens is you have a discussion with the client to discuss how much budget they have for PPC. If it is enough, then you go through which keyword campaigns will cost what, and then you charge your fee ontop of that. PPC only really suckers in the large companies who piss money up the wall, not one to bother offering sole traders and small independents. PPA might be more up their street.