Yes, Renfe's website is a bit of a hassle to use, but the discounts are substantial. If you do want discount advance tickets, here are my tips:
1) You will need the invaluable tutorial from TripAdvisor: http://tinyurl.com/cu48wk5
2) To find all connections for your Toledo to Madrid to Seville route, you should first look on Bahn (German rail) http://reiseauskunft.bahn.de/bin/query.exe/en, using Rick's advice: http://www.ricksteves.com/travel-tips/transportation/trains/online-schedules
For some reason, when I needed to go from Toledo to Madrid to Barcelona, the Renfe site only showed two connections that day, while the Bahn site showed many. I ended up booking Madrid to Toledo round trip, then a separate ticket Madrid to Barcelona, with one hour in between. As a bonus, the Madrid to Toledo ticket had a slight discount for round trip.
3) Don't even try to use your credit card to buy the ticket on Renfe's website - use PayPal from the get-go.
In the end, I was able to book the tickets, but I realized it took me FIVE websites to do so (Renfe, Bahn, PayPal, TripAdvisor - and Rick Steves to tell me about the others!) It did work fine after all that.
And no matter how you book your ticket, changing in Madrid Atocha Station from your inbound train from Toledo to your outbound train to Seville may require changing levels. If it does, ask for the elevator connecting the departures lounges; if you use this elevator, you don't have to go through security again and you won't get lost (so definitely preferable to the alternative).