I don’t know how to solve the problem of marks in Hebrew, in Glyphs. I don’t know how to write opentype correctly so that characters that have a smaller mark also have it in after adding additional marks. Is there a solution or have I simply overlooked a very simple thing?

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Welcome to the club. Either there is reordering in the shaping engine you can rely on (I don’t know, but doubt it for Hebrew), or you have to cover various context possibilities like glyphname @marks @marks @marks @resizeablemarks'. You cannot use IgnoreMarks flags for substituting marks, unfortunately.

In which opentype feature should I write it so that it will work?

That could be done with mark filtering.

lookupflag UseMarkFilteringSet @resizeablemarks;
sub glyphname @resizeablemarks' by @smallmarks;
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Thank you, I think it will work.

I don’t know if it’s worth noting but if I used character and mark substitution to composites in ccmp or liga, in Text Preview all the characters display correctly even with the additional marks, but at the same time it didn’t work in InD.