You can use the same capillaries. We have AB 3130 and we use it for both the applications. Its always washed right before a cycle. 

We use 50cm length, it works good for both. although we do gDNA, but we have done mtDNA too. You could give a formamide wash too if you want. Just use 9uL formamide in all wells and run a test run. 

For genotyping we use, FAM, VIC, NED, HEX etc. 

Kalpita

Thank you my Dear Kalpita.