I have the same problem. I book my easyJet flights in bulk to save on administration fees. On some flights I require checked baggage, on others I don't. Unfortunately the easyJet booking system doesn't allow customers to add extra services to specific flights- it's all or nothing.
It appears to be a quirk of the system rather than a money making ruse. It is possible to add extra services (e.g. baggage or sports equipment) after you've flown your first sector (or two), but you have to add them to ALL future bookings- very annoying.
Whatever you do, DONT pay at the airport. It is far more expensive than prebooking online. It's probably cheaper and easier to just bite the bullet and pay for both sectors before you fly, frustrating as that may be.
Hopefully there's a workaround solution to this problem which I haven't come across but I doubt it