Played until I got permastuck in Brinstar. So far it seems like you just added/or replaced tiles in certain rooms and opened paths early, with no other alterations.
i use SMILE,but when i insert Missiles, i can't take this missile. Samus don't wanna take it
To clarify a little more on rolando's comment- PLMs are things like door caps, map/save stations, and the scroll arrows. Right click on any of those and you can change it to whatever other PLM you want it to be, which can include Missiles, Supers, PBs, the suits, or any other item you aquire.
The begining of the help faq I believe explains it a little better.
What you were doing was place tiles, not items. Those tiles are what the missile pick-ups will look like. If you canged those tiles, the missiles would look just like them. I hope that made some sense...
In short: The PLMs are interactive things in the game. Door caps, item pickups, gates, etc. The things in the tile table (when you choose the tiles you want, at the bottom) are simply what the game will look like. They don't do anything, but sit there.