I was going to reclass her, but also I want her to be a sage. What should I do? I'm on Arc 2, and I just completed the level in which you unlock Henry. It's not that I don't know who to use a Master Seal on, it's just I haven't decided on what to do with Lissa yet.
It doesn't matter.
You can reclass or promote any character including those with a unique class as often as you want, as long as you have a Second Seal (reclassing) or a Master Seal (promotion). Those can be bought freely from merchants and are very affordable.
You can even use the Second Seal to demote a character if you wish. Any stats lost in the process due to lower stat caps are awarded back on promotion.
Since reclassing resets the character's level to 1 but not his/her stats, you will eventually reclass your characters a lot in order to make them learn useful skills and maximize their stats.
Simply experiment with reclassing until you've decided which class you want to keep Lissa in. By then, she'll be an extremely powerful asset in your army, assuming you're still using her.
It's a little subjective because there are so many reclassing options in Awakening, but Lissa is designed to be a good healer, so you would benefit to keep her in a class that can use staves. Sage is a good option as well as Falcon Knight.
If you just want to obtain more skills, you can reclass her to any number of other classes before finally upgrading to a Sage or Falcon Knight. Naturally this takes a lot more time and training investment.