Before checkin: only upfare is possible. This is basically the operator reissuing your tix on a W / J fare. You'll pay the price difference up to what that fare is in your desired travel class at that moment. You should see this option on AFKLs websites (NOT in the apps, NOT in the mobile versions of the website) but in my experience this applies only to itineraries ticketed *and* operated by AFKL. If you have one or more segments operated by other airlines, the upfare options will not be visible in the "Manage my booking" section. This gives you some flexibility in upgrading outbound and / or inbound legs but *NOT* individual segments for connecting flights (i.e. -flying WAW - CDG - JFK - CDG - WAW, sold by AF and on AFKL metal, you'll get the option to upfare the WAW-CDG-JFK leg and / or the JFK-CDG-WAW leg but *NOT* the CDG-JFK or the WAW-CDG segments).
Upfares means you get all the benefits associated with this new fare (i.e. - miles, XPs etc.)

At OLCI / checkin: if available you'll receive the option to upgrade your seat. This could be in-app, while selecting sets, at the airport, at the gate, or on board. Ranges and prices vary greatly and there are topics in this forum with references from other travellers. You can pay with cash and / or miles.
Upgrading at checkin means you'll receive the benefits associated with the initial fare / ticker (i.e. -you bought an eco tix then upgraded from eco to business at OLCI, you'll receive the XPs for your original ticket, same for bagage allowance)