Yes, you pay for the amount of seconds you use (up to 2, up to 15 or up to 60 seconds) of a song. If you buy a 15 second sample, you can sample 2 seconds from the first part of the song, 9 in the middle and 4 in the end if you want to (2+9+4=15). The total sampled time is counted as cumulative (the sum total of the parts of the song you have sampled), it doesn't need to be continuous.
So you can choose which parts you want, as long as they add up to max 15 seconds for that type of sample. Same goes for the licenses for samples up to 2 seconds and up to 60 seconds.
You need a separate sample license for every individual song you sample from.