Look, here's how to set up Under Combos AND Secret Combos:
Under Combos:
1: Find the tile you want to be the under combo. Press + and - until you find the right CSet you want for the tile.
2: Go to Data>Under Combo, and click set (or something like that).
Done.
Secret Combos:
1: Go to Data>Secret Combos. Click on the tab for the appropriate flag type you wish to use (Hammer, Wand (Wand MAGIC is in the Magic tab, while this is the actual Wand, not the magic), Strike, Hookshot, Stairs, and Reflected Fireball are in the Misc. Tab, as are Flags 16-31), and click on the box for the flag used. If you're using Burn Flags, remember that "Blue Candle" is Flag 4 (Burn (Any)), Red Candle is Burn (Red Candle +), Wand Fire is Burn (Wand Fire +), and Din's Fire is just that- Burn (Din's Fire), which I believe doesn't work, not even in 2.11. Also remember to press + and - while selecting the tile to change its Cset.
2: Place the appropriate flag wherever you want it (if you haven't already). Remember that Flags 16-31 (Secret Flags 1-10) are in the Misc. Tab of the Secret Combo editor, and are only triggered by Trigger Combos, the Enemies->Secrets flag, and Trigger flags (Burn, Sword, Strike, etc.. In other words, flags that activate when you use one of your items on them.).
Remember, if you remove a combo by its combo type, you use Under Combos. If you use flags to change the combo, you must use Secret Combos. The exception? Flags 16-31. If you place those on a combo that you slash to get rid of (Slash, Slash->Item, Bush, Flowers, and Tall Grass), it'll use the Secret Combo for the corresponding flag instead of the undercombo (Technically, it uses the Under Combo, but at the same time, that's overwritten by the Secret Combo). That's a good way to have multiple under combos on one screen. I think your problem was that you were using Flags on the combo instead of Combo Types.