Copy the files "iplrom.x1t", "font0808.x1", "font0816.x1" and "font1616.x1" to the same folder as advtool.exe
Then copy the game (like "Super Mario Bros. Special.d88") to the same folder, and rename it to FDD0.d88 (and FDD1.d88 if there are 2 discs).
Then run advtool.exe. It will produce the rom file (xmiladv.gba).