Well, I can kind of overview it for you...
Effectively Phoenix's tools simply run in any web browser that supports JavaScript. I think I found Chrome or FireFox to be ideal. Once you download the tools you open the HTML page into whatever browser you want to use.
From there when you go to the map editing feature you are presented with your choice of the various different tilesets and the maps for various places are able to be chosen and will load with the default tileset. Each map has a set size limitation based on how many bytes are available for that map in the FF-II ROM. If you go past the expected size in your modification of the map then you will not be able to fit your new map into the space the old one occupied so you have to be aware of that value as you work; IIRC if you exceed the expected limit the value turns red or something. Otherwise you go nuts changing the maps to your liking. IIRC if you access a map that says something like "Load map (0 bytes)" then that map is just an empty map it's probably just a 00FF sequence in the map block...again it's been a while but that's what I remember.
Putting the modded map in your ROM requires a hex editor. The map tool generates a HEX string which is the data for your map that needs to go into the ROM. You have to find the starting and ending offset for the block of data in the ROM that represents your map (IIRC these are listed in the editor for each map, or at least the starting offset is and the size of the data so you can calculate from that). Then you pretty much simply copy and paste the modded map HEX string into the ROM over the top of whatever map you're replacing. I highly recommend backing up your modded ROM master, applying the modded map, test the map to make sure everything works, and then move forward with further modifications so that way you keep everything clean.
Although Phoenix's tools make it very easy to mod the graphical map hex data, there are other things you can do which require pure HEX editing skills. Such as change the tileset the map uses, the background image, if it uses the parallax effect, and the event trigger locations for maps (that is where doors and treasure chests appear, as well as actual event triggers such as when you walk into a room and an event occurs -- for example when you enter the top of the Damcyan castle the event trigger with Anna's death and the Spoony Bard routine happens). However you 'll have to investigate the event data and map data. I believe this is all documented in some of the offset resources elsewhere on the site, I don't remember exactly where all that is at the moment. But if you've downloaded the offset information that many people have generously donated here you should be able to find that pretty easily.
Also one thing I did find when I was modding maps is that the map data uses a fairly simple compression technique to save space when you have a horizontal row of the same tiles. This is why you see in my screen caps above that I've run the wall tiles all the way across the screen even though you'd never see that. Effectively it allows you to save space and have more bytes to play with for what you really want to do. One effective technique then is to overwrite the map with horizontal rows of the same tile and then go in and start making the playable area by overwriting the tiles. You'll be surprised how some very small maps can be expanded within the limited space or have more details added (like bookcases, beds, chairs, wall sconces, etc...) when you do this. It's not quite as aesthetic as having the cleaner outlines of the room but in some cases the richness of the new map outweigh that IMO.
We have EVEN MORE themes now, but some old ones are gone...