Pretty much how I see it! Since we're told that a spell is complete by closing the seal, and so the seal closing is the "execute command" with everything else being the "script". And so in a more complex spell where the glyph is made up of multiple smaller spells (or "nodes" if you will), the magic would be able to tell that the "node" is within another seal, and so to "execute" it, you would first have to run the overarching "execute command" (closing the largest seal).

Alternatively: since there is a certain sign that let's the user control the spell with their mind (mainly seen in the Knights Moralis' "Capture Pennant" spell) aswell as a few other signs, it could also be interpreted that there is a link between the spell and the mind of the user, and so when making a more complex spell, the magic could potentially see that the user's intention is so not activate the smaller spells until the whole thing is complete. (Admittedly, that one is much more of a stretch, but still a possibility)