Can anyone tell me how to know which prefixes go before which prefixes?

For exmaple... "patro" is father, and "ge-" is the prefix meaning of both sexes, making "gepatroj" the term for 'parents'.  "bo-" is the prefix for related by marriage, making "bopatro" to be 'father-in-law'

How do you term 'inlaws' (plural, of both sexes) then? do you combine both prefixes into the same word (bogepatroj) to make "inlaws", and if so which prefixes come first.. is it bogepatroj (related by marriage, both parents) or gebopatroj (both, related by marriage, parents)

Or does the order really not matter as long as both prefixes are in there

Prefix order only matters occasionally.   In general, start from the root word and work your way out.  So a "malsanulejo" is a hospital: we have san/a (healthy), then we add mal/, for mal/san/a (unhealthy), then mal/san/ul/o, an unhealthy person.  Finally, mal/san/ul/ej/o, a place for unhealthy people.  If we switched the order, the meaning could change.  So a "malsanejulo" would be a person from an unhealthy place.  In the case of the in-laws, it seems to me that there isn't a huge difference in meaning, whether you use "bogepatroj" or "gebopatroj".  But personally I think "bogepatroj" makes more sense, so that's the word I'd use.  There is rarely anything between ge/ and the root word, since in most cases it wouldn't make sense.

- Erin