How do I know if my cats are getting along?

I have a 1 year old cat, Abacus Finch, who I recently got a companion kitty for, Elphaba, who was 5 weeks old when we got her. She had a pretty bad respiratory infection and was in quarantine for a few weeks in our bathroom. At first Abacus kept hissing at her, and me when I smelled like her. But while she was locked away, he'd lie by her door and make this noise like a pigeon. Now that she's out and about, he tries to lick her all the time. She doesn't want him to so she runs, and then he chases her, causing her to hiss, meow, and/or hide under furniture. Is he being aggressive towards her or is he trying to be nice and she reacting badly? I'm not sure what to do and whether to break them up or let them work it out. I worry a lot because he is part maine coon and weighs about 14 pounds. She weights 1 pound and I don't want her to get hurt. Sometimes it looks like he's biting her, but just so that way she sits still. What should I do? Are they getting along? Should I separate them when they start this?