Two methods, really. One was using Tile Layer Pro which, while not as versatile as TM, still works pretty well. Since I can't choose to interleave tiles, however, I had to place tiles in the Arranger first, then edit them with the arranger in mind.
Second, somewhere between madness and boredom, is to find out where these images are stored in the ROM with a hex editor, see their values and then edit accordingly the values related to certain colors. This one is more trouble than it's worth, but works. I made a copy of the ROM, edited the copy, then compared both in Hex Workshop to see where it was using transparency instead of solid colors.
Both ways worked pretty well in the end. It's the first game I've (almost fully) translated!
It's somewhere around 90+something translated, because I won't be handling things like sound (i'd love to change soundbytes like "Answer the riddle", etc. but have no idea how to) or the main screen title (I could translate "Light Crusader" but, really, it's not worth it). The "Computer Designed by Treasure" is also there, I decided to leave it as a sort of "signature" by the studio (since, in order to bring up the fact I did the translation, I had to edit the end credits and steal Sega's thunder, along with shortening the same line again about Treasure).
Now, it's back to working on Link's Awakening and going mad with Zero Mission's tilemaps!