Hey @owynter.
May I ask you why you didn’t ask for some help when getting stuck?
There is the amazing support channel and there are 2 community platforms.
I know it can get very frustrating as soon as something doesn’t work out as intended. Trying too long to make it work often leads to even more frustration.
Developing a feeling when additional help is required (after I tried enough) is something which helped me a lot to avoid such situations.
Regarding your issue, modals (the container where you place your content) are regular divs which you treat as always, except the block specific options inside the primary tab. You need to keep in mind that there are transitions/transforms applied. So in case you want to apply these properties to the modal, make sure to wrap your modal content inside another div.
Padding, margin and scrolling will most likely start to work as soon as you apply overflow:auto to the modal block.
I assume there was simply not enough space available to make margin/padding work because of the lack of scrolling ability.
So, it was actually only one line of information which was required to fix your issue. Not a big deal, right?
It seems you are enjoying the general workflow with Cwicly. You are not the only one who get stuck here and there.
Just ask for some help next time to avoid frustration and losing valuable time. When it comes to design stuff, one or two applied/adjusted options inside the block editor are sufficient in most cases.