Yes, music copyright holders are notoriously demanding in what they'd charge. Which is why that the usual advice with song lyrics is simply not to go there.
The fact that you're only quoting bits of lyrics in most places doesn't make a difference: if what you're quoting is a direct and recognisable use of the words, you're in breach of copyright if you don't get permission
Having said that, you don't need to get permission when it's in manuscript (unless you put it out on the Net or some such) until you've got a contract to publish it. It'll be in the contract that you clear the permissions and pay for them, and you have to sign that you have. And your editor will probably remind you to do it, as the publisher is jointly liable with you if the copyright holder sues... It can take ages, too, so if you get a contract you need to get onto it straight away, too
I suggest you get hold of the Society of Authors' leaflet about clearing copyrights, which gives you the details.
http://www.societyofauthors.org/guides-and-articles