There are audio guides, after you select the main product you will have the option to add an audio guide.
The time pass is a bit confusing, in the context you see, they are talking about timed entry to the special exhibition(s) which oddly may, or may not have an extra cost (the current one does not). If you do not choose the exhibition, you will later be asked for an entry time to the general collection. However, if you pick a time for the exhibition, you do not select a time for the general collection. I guess the assumption is, you go see the exhibition at the appointed time, then the general collection after at your leisure.
You can walk through the purchase several times, choosing different things, to see how what you select changes things.
By the way, another thing offered in the checkout process is a guided tour, in English. It is a 90 minute tour of the main pieces, but only offered at 11:00 and 1:00. At 10 euro, that's a bargain if it works for your schedule.
As for the Prado or the Palace, it comes down to interest. I would certainly recommend the Prado...but my Wife for example would choose the Palace.