You are not going to get Brutal Doom to run through PrBoom. That mod requires a GZDoom or Zandronum; neither having ports for the 3DS. However, there is a mod called
Boiled Doom, which attempts to recreate Brutal Doom for vanilla Doom so that in theory should work.
For Sigil (assuming you downloaded it from
rome.ro), you need to use the "COMPAT" version if you want to run it in ports that don't support MAPINFO such as PrBoom3DS.