Your best bet is to take the Malpensa Express to either Milano Centrale or Milano Porta Garibaldi, and from there take a high speed train to Firenze. This can be either Trenitala's Freccia Rossa from Centrale, or Nuovo Trasporto Viaggiatori's Italo leaving from Porta Garibaldi. All the links provided allow you to book the tickets in advance. The reason you can't book everything via one website is because the train lines are operated by different companies: Malpensa is a Trenord station, whilst Milano Centrale and Porta Garibaldi are both FS (national railway company) stations.
All in all it's always good practice to book national trains (the various Frecce operated by Trenitalia or the various Italo routes) in advance. The reason being that on these a seat reservation is required for each passenger. More importantly, the last minute fares tend to be very steep. Regional trains on the other hand, be it Trenord, some other local company, or any FS interregional route, sometimes don't require a seat reservation. Hence tickets for the latter can be easily purchased on the day since you can travel without sitting down. When it comes to interregional trains however it is sometimes not possible to reserve tickets in advance (the Malpensa Express being a notable exception to this rule).
Since you are worried about missing train connections, note that advanced tickets for the Malpensa Express can be used up to 4 hours after the booked departure time. Trenitalia and Italo both offer exchangeable refundable ticket fares which are of course more expensive than their non-exchangeable counterpart. To avoid any bad surprises you can book the latest sensible train, say 5 hours after you land, and attempt to exchange the ticket at the station to board an earlier train, should your journey from the airport take less than expected.
