in my original config for claymore I have each miner name if I was to use custom file upload it would upload each miner in awesome miner with the same worker name I have set up in claymore right? How do I fix this
You should define the pool and worker name in Awesome Miner. It's only the software itself that you upload to remote computers - any configuration file you upload will not be used. Awesome Miner controls all that for you.
It's in Awesome Miner main application you define your pool and mining settings. On each remote computer you will run Awesome Miner Remote Agent that will start the Claymore miner with correct pool and other parameters.