System Transfer

Hi!
Is this possible to System Transfer from my old 3DS without Capture Card to New 3DS with Capture Card (and NAND mod) ordered here? I mean by using Nintendo built-in System Transfer Tool. Is it even possible? Will it mess with capture software? Sorry im completely newb on that matter.
Is this possible to System Transfer from my old 3DS without Capture Card to New 3DS with Capture Card (and NAND mod) ordered here? I mean by using Nintendo built-in System Transfer Tool. Is it even possible? Will it mess with capture software? Sorry im completely newb on that matter.