Those two options do different things.
And I do not understand what you mean by "ignore the permission settings", so I cannot advice, which one you should use.
What is your actual problem?

Hi, I had the script generated below as I wanted the transfer to ignore the permission settings. I also read somewhere in this forum you can use the -nopermissions switch. Can someone advise which is the correct method?
Thank you

Script 1
lcd C:\MARS\Mars Export\lan\archive
cd /Inbound/MY/MARS

put -rawtransfersettings[1] IgnorePermErrors=1 -filemask="*.csv>=1D" *

exit

Script 2
lcd C:\MARS\Mars Export\lan\archive
cd /Inbound/MY/MARS

put -nopermissions -filemask="*.csv>=1D" *

exit