Personaly I use parts out of UML, PHP does support some OO features. Anyway basic software engineering practices are not langauge specific, you should be able to model an application/system and apply it to many languages.
Look at 'use case' it one of the most useful and easiest.
Also ER diagrams come in handy when modelling databases. (I know MySQL doesnt support it, but the same basic princables apply).
Remeber UML is not strict, you should just take ideas from it and apply your own way of thinking.