Memory card on which recording was originally done should be considered primary evidence and pen drive as secondary evidence. Memory card itself needs no 65B Certificate. If you intend to file a printout of the contents of the memory card, you need to file a Certificate under Section 65B. I don't understand the point of filing another USB drive having the same contents as the original memory card...if that USB drive is only as a copy given to other party, there is no need to give any 65B certificate with that.
Having said that, knowing the 'proficiency' of our judiciary with electronic records, my suggestion would be place a printout of the contents on Court record along with a 65B certificate anyways to save your evidence from any future technical loopholes.
CBI v . Dev Raj
CC No. : 07/2013
Delhi District Court
Judgment: 31 May, 2016
"(M)emory cards have been duly proved during the trial. Since, all these memory cards are the original memory cards, in which the conversations were directly recorded, these memory cards are the 'primary evidence', and no certificate under the Provisions of Section 65B of the Indian Evidence Act, is required to be furnished by the prosecution to prove these 'documents'."
For signing the Certificate, you are in fact THE best person to sign such a certificate being the person under whose control and possession the eletronic record was.
And you don't need to be present for filing such certificate (at filing: no, at evidence: yes, of course and be ready to be grilled on it); in a High Court filing is done across the Registry even by Court Clerks and in District Courts, the Advocate alone can file it across the Bench.
EDIT: Well I had to read your query some four times to get the hang of it. You mean the Lab johnnies tested the contents as contained in the USB drive? In that case, I'd suggest you file the USB drive also (in addition to the memory card) with a 65B Certificate under your signatures, Affidavit of the technicians; if possible, try to give some unique identifying feature on the USB drive, probably something like a unique Company logo or something so your witness may be ready to testify that he can identify the USB drive as the one used for testing (and btw, is the technical guy really ready to depose in Court?).