I just use the IDE, have for years now. It's got more features than any map editor ever.

I think I did a blog post about this ( Done so many they blur into one ), but for Outpost I have every level in it's own mc.
From there I have a background MC, which is the floor, a walls mc, an objects mc ( Baddie start positions as well as things like chairs / tables etc. ), a vector mc ( Which is just the rectangles for Nape ) and a shadow mc.

When it comes to plotting I create lots of 600x600 bitmaps ( Megatiles ). I then split the mc's up and burn them into the bitmaps, so both the walls and background are in the same bitmap ( Shadows are separate as we overlay them on top ).
I did a similar thing in Knights Quest, it means even though you snap to grid so it's like tile based, it's much more art based. For example we can use a font and write text on the floor, put a filter on it, rotate, whatever and it doesn't cost us anything in cpu time as it's just a bitmap when we display it.

When plotting the walls I keep a record of them, and setPixel into a small bitmap ( So each 32x32 wall tile is 1px in this bitmap ). I then use that for path finding etc. ( Like the usual 2D array, but just in bitmap form, does the same thing ).

It's a case of using the strength of tiles, ie simple collisions and path finding, but trying to vary the graphics as much as possible so it looks a lot more art based.

Squize.