Phonetic glyphs stood for simple consonant-vowel (CV) or vowel-only (V) syllables.
However, Mayan phonotactics is slightly more complicated than this.
Most Mayan words end with consonants, and there may be sequences of two consonants within a word as well, as in xolteʼ ([ʃolteʔ] 'scepter') which is CVCCVC.
When these final consonants were sonorants (l, m, n) or gutturals (j, h, ʼ) they were sometimes ignored ("underspelled").
More often, final consonants were written, which meant that an extra vowel was written as well.
This was typically an "echo" vowel that repeated the vowel of the previous syllable.
For example, the word [kah] 'fish fin' would be underspelled ka or written in full as ka-ha.
However, there are many cases where some other vowel was used, and the orthographic rules for this are only partially understood; this is largely due to the difficulty in ascertaining whether this vowel may be due to an underspelled suffix.

Lacadena & Wichmann (2004)  proposed the following conventions:
A CVC syllable was written CV-CV, where the two vowels (V) were the same: yo-po [yop] 'leaf'
A syllable with a long vowel (CVVC) was written CV-Ci, unless the long vowel was [i], in which case it was written CiCa: ba-ki [baak] 'captive', yi-tzi-na [yihtziin] 'younger brother'
A syllable with a glottalized vowel (CVʼC or CVʼVC) was written with a final a if the vowel was [e, o, u], or with a final u if the vowel was [a] or [i]: hu-na [huʼn] 'paper', ba-tzʼu [baʼtsʼ] 'howler monkey'.

Preconsonantal [h] is not indicated.

In short, if the vowels are the same (harmonic), a simple vowel is intended.
If the vowels are not the same (disharmonic), either two syllables are intended (likely underspelled), or else a single syllable with a long vowel (if V₁ = [a e?
o u] and V₂ = [i], or else if V₁ = [i] and V₂ = [a]) or with a glottalized vowel (if V₁ = [e?
o u] and V₂ = [a], or else if V₁ = [a i] and V₂ = [u]).
The long-vowel reading of [Ce-Ci] is still uncertain, and there is a possibility that [Ce-Cu] represents a glottalized vowel (if it is not simply an underspelling for [CeCuC]), so it may be that the disharmonies form natural classes: [i] for long non-front vowels, otherwise [a] to keep it disharmonic; [u] for glottalized non-back vowels, otherwise [a].

A more complex spelling is ha-o-bo ko-ko-no-ma for [haʼoʼb kohknoʼm] 'they are the guardians'.
A minimal set is,
ba-ka [bak]
ba-ki [baak]
ba-ku [baʼk] = [baʼak]
ba-ke [baakel] (underspelled)
ba-ke-le [baakel]
Phonetic glyphs stood for simple consonant-vowel (CV) or vowel-only (V) syllables. However, Mayan phonotactics is slightly more complicated than this. Most Mayan words end with consonants, and there may be sequences of two consonants within a word as well, as in xolteʼ ([ʃolteʔ] 'scepter') which is CVCCVC. When these final consonants were sonorants (l, m, n) or gutturals (j, h, ʼ) they were sometimes ignored ("underspelled"). More often, final consonants were written, which meant that an extra vowel was written as well. This was typically an "echo" vowel that repeated the vowel of the previous syllable. For example, the word [kah] 'fish fin' would be underspelled ka or written in full as ka-ha. However, there are many cases where some other vowel was used, and the orthographic rules for this are only partially understood; this is largely due to the difficulty in ascertaining whether this vowel may be due to an underspelled suffix.
Lacadena & Wichmann (2004)  proposed the following conventions:
A CVC syllable was written CV-CV, where the two vowels (V) were the same: yo-po [yop] 'leaf'
A syllable with a long vowel (CVVC) was written CV-Ci, unless the long vowel was [i], in which case it was written CiCa: ba-ki [baak] 'captive', yi-tzi-na [yihtziin] 'younger brother'
A syllable with a glottalized vowel (CVʼC or CVʼVC) was written with a final a if the vowel was [e, o, u], or with a final u if the vowel was [a] or [i]: hu-na [huʼn] 'paper', ba-tzʼu [baʼtsʼ] 'howler monkey'.
Preconsonantal [h] is not indicated.
In short, if the vowels are the same (harmonic), a simple vowel is intended. If the vowels are not the same (disharmonic), either two syllables are intended (likely underspelled), or else a single syllable with a long vowel (if V₁ = [a e? o u] and V₂ = [i], or else if V₁ = [i] and V₂ = [a]) or with a glottalized vowel (if V₁ = [e? o u] and V₂ = [a], or else if V₁ = [a i] and V₂ = [u]). The long-vowel reading of [Ce-Ci] is still uncertain, and there is a possibility that [Ce-Cu] represents a glottalized vowel (if it is not simply an underspelling for [CeCuC]), so it may be that the disharmonies form natural classes: [i] for long non-front vowels, otherwise [a] to keep it disharmonic; [u] for glottalized non-back vowels, otherwise [a].
A more complex spelling is ha-o-bo ko-ko-no-ma for [haʼoʼb kohknoʼm] 'they are the guardians'. A minimal set is,
ba-ka [bak]
ba-ki [baak]
ba-ku [baʼk] = [baʼak]
ba-ke [baakel] (underspelled)
ba-ke-le [baakel]
Maya script