So you're using
this base right? Although it doesn't say so in the thread, this base seems to have
JPAN's hacked engine installed, which handles healing places differently.
You now have to use the variables 0x405A, 0x405B and 0x405C to determine the position where you end up. To choose the map, put setvar 0x405A 0xmmbb, with bb being the map bank and mm being the map number. So for example, if you want to get warped to Cinnabar Island's Pokémon Center (12.5), you'd have to put setvar 0x405A 0x050C. Likewise, use variable 0x405B for the x-coordinate and 0x405C for the y-coordinate on the map.
Hope this helps!