I am putting a piece one of my friends wrote for our middle school band into Sibelius to format the parts and score correctly. The rests are, currently, all quarter rests. Should I change these to half rests whenever there are two in a row or are there times when I should leave them as two quarters for the purpose of clarity/counting? Most of what I'm asking about are pairs of rests on 1,2 and on 3,4 of 4/4 measures.
Pairs of quarter-rests that add up to half a bar should be changed to a half-rest. That applies to your 1,2 and 3,4 beats situation.
But rests should not usually be combined across the middle of the bar, so quarter rests on beats 2,3 should be left as they are.
But there are no "unbreakable rules" here - if it's easier to read a part where a bar is written as quarter-note, half-rest, quarter-note, then write it like that.
In 4/4 or 2/2, two quarter rests spanning the first half or second half of the measure can be combined. It's generally hard to sight read a half rest spanning the middle of the measure. It's a tradition but it really makes things easy to read.
In 6/8, I've never seen half rest. I have seen half rest spanning beats 1&2 or 2&3 in 3/4 time (mostly the former). In 6/2, only pairs of beats 1&2 or 3&4 or 5&6 are spanned by half rests.
The general rule is that rests (and notes) should reflect the time signature. Irregularities are generally indicated by slurs to mark phrasing.