runouw.com

I'm struggling hard to figure out how to place items like Thwomps, Flipping Platforms, Pendulums, Flame Towers, Warp Pipes etc. in the right place. It would be helpful if you could make a list of these items in ascending order of danger.

I don't have a clever response right now except that you should use the Ctrl button to move these items within an 8x8-grid, and all other items generally too. Any placements of items outside of this grid should happen due to finetuning, etc. placing a bushy tree on the floor so that only its trink can't be seen.
If you don't know exactly where to place a flipping platform, pendulum etc., just playtest and try out until you get it right. It's not that hard.

On a side note, placing platforming items (aka green platforms, blocks, logs, floating platforms, flipping platforms, pendulums, clocks) takes some time, depending on the loading time of the level, so if you're making a very big level with a very huge loading time, use the download version for placing these items in order not to risk an AFP crash. This also applies for deleting items with the eraser tool.

Pretty much everything Supershroom said applies to your problem.

Although it's a bit late to give criticism about SM63 as it was developed years ago and likely won't be updated (unless if Runouw has some secret hidden plan up his sleeve, but that's not likely since he's working on Last Legacy).