If I install excavator and ubuntu 16.04 on my 1070s will excavator still be able to control the clocks just wondering I'm not a linux guy but trying to learn it more than my second question is on my win 10 pro build do I just leave out the clock commands to let AF manage my cards I'm asking because I read somewhere that running excavator would disable msi AF or this is no longer the case
Excavator will not disable MSI Afterburner, you can manage your GPU settings either using command line or third party software (e.g. MSI AF).
Regarding Linux, yes you will still be able to manage GPU through excavator's commands.