Put simply, what determines how mayan glyphs are arranged?
Mainly appearance, though some glyphs are more common in secondary form (I forget the actual term for the skinnier glyphs on the edges of blocks), and others need to be the main glyph in a block.
Different scribes had different preferences. Some tried to keep individual words together in a block. Some gave more space to complex glyphs so they didn't have to make the details as tiny. (I avoid making 'tz'i' small. Too much work.) Some would emphasize important parts of the writing by giving it more space. Names usually get a lot more space the first time they show up, and are then compressed in later appearances. Some scribes used one glyph a block - either because they weren't comfortable enough with writing to play with it, or because they were using a special, extra fancy variant that turns each glyph into a full person who takes up their own block.
Glyphs that stand for full words are usually in the same block as their phonetic compliments (the glyphs that tell you their first or final sound).
Numbers and 'ʔu-' (which means 'they/it/he/she') are usually first in a block (at the left/top), and I've never seen 'ʔu-' alone. On the other hand, 'w-vowel', 'ni,' and 'TE' glyphs are usually in the final position (right or bottom).
Often, a set amount of space for the writing was decided beforehand, and scribes did their best to make the writing fill that space.
'ʔu-' means he/she/they/it, and I've never seen it on it's own, or in any non-initial position in a block. (It's always either the left side or the top.) Glyphs that stand for 'w-vowel,' 'ni,' and 'TE' are usually, but not always, in the last position (right side or bottom).
Reading order is from top left of a block down to the bottom right.
Glyphs that stand for full words are usually in the same block as their phonetic compliments (the glyphs that tell you their first or final sound).
While some scribes stack secondary glyphs, that isn't common. (Usually there aren't 2 skinny glyphs on the same side of a block.) Main glyphs are fine to stack, though, and having a secondary glyph on multiple sides is common. (Also, some secondary glyphs have half versions, so you can stick 2 together in the same spot.)
The amount of variation is breathtaking. Some monuments have glyph-blocks so big and complex that entire sentences fit in one. More casual writing on cave walls usually consists of 1-3 glyphs a block. And monuments can also have really simple blocks. It's up to the scribe.
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On a larger scale, blocks of glyphs are USUALLY in horizontal pairs (left to right). These pairs can then be laid out in any order you want. The whole text can be horizontal, the pairs can be arranged vertically, they can start vertically down the side of an image, and then continue horizontally underneath it, etc.
You also get single columns, rather than pairs, and even glyphs being read from right to left.
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In summary, it's mostly personal preference. Even glyphs that usually fit in a certain spot can be stretched/squished into another if the scribe really wants them to.
But once you figure out the writing style of the scribe (or your own writing style!) it's often possible to predict roughly how things will be laid out.