That's not even the answer to the first question he was asking, ZM. You have to combo cycle to make spikes like that work. You can either set 1 combo for each frame of the animation, or save space by just having 1 combo for damage and another combo for no damage that link to each other and both animate. I'll explain the latter method right now.
First, make the damaging combo, for when the spikes are up. Right click an empty combo(a red square with a black border) in the box on the right of the screen. Set the tile to the first tile of the spikes coming up by clicking the first box in the row of boxes at the top of the window, then just find the spike tile in the tiles page. Next, put the number of tiles that the spikes are going to be up for in the "A.Frames" box. The spike tiles have to be next to each other in the list of tiles for it to work right though. Finally, set the type to "damage" whatever. You're going to have to play around with the "A.Speed" number yourself to find a speed you like for these going from down to up to down again, but set it to 10 just to start out. Now click OK.
Right-click the next blank combo in the box on the right side of the screen, which should be right next to or below or something like that, the one you just made. It should be nearby it just to make it easier, though it really doesn't matter if it's on a different page or something, it just gets more confusing then. Again, set the tile, this time to the first tile of the spikes being down. You need at least 2 tiles of the spikes being down for this to work, so if you only have one, copy it and paste it next to itself. Then set the "A.Frames" to 2, and try setting the "A.Speed" to something around 50, to give the player time to walk across it while the spikes are down. Again, you're going to have to play with this to find a timing you like. Now click the box under "Next" to set the next combo, and then find the combo for the spikes going up then back down, and click "Done", then click "OK".
Edit the spikes up combo again and link it to the spikes down combo in the same way you just linked the spikes down to the spikes up. Now place one or a few of the spikes up(or down, it doesn't really matter) combos on a screen, and save the quest, then go test it out. The spikes should go up, then down, and then stay down for a few seconds, then go back up. Whew, that was probably a lot longer than it needed to be, but I'm specific about things, so, lol.
To answer the other 3 questions, number 2, yes, but I don't quite know how myself(I'll play around and if I figure it out, I'll tell you), though I know it has to do with linking secret combos to each other. Number 3, as far as I know, you cannot set a flag to an under combo. And finally, setting the Wizzrobes to enter from the sides IS the way to delay them like that, but at least 1 tile on one of the sides of the screen has to be walkable for it to work. Just put a walkable tile in the corner of the room and draw the corner on a layer for the screen.