So if they're allophones, they're not contrastive phonemes. That makes things simpler, though. The idea that a dialect would sometimes spirantize its stops is very familiar.
If that's the extent of variation between dialects, I'm not sure what you're asking exactly, since producing an orthography seems to be a relatively straightforward issue of choosing glyphs that will be easiest for people to use. Most orthographies don't represent allophones anyway.