I’m totally lost when it comes to augments. Certain things don’t seem to transfer.

Eventually an item called a Mark Receptor will be released but until then no, it can not be transferred.

Yeah you need a receptor

So should i keep all my weapons that have the mark affix ?

don't need, mark augments are pretty common so you gonna find tons of then all the time

@Jamesmor oh i see, thank you for your prompt reply