I just transferred my brokerage account to Vanguard and had the same question since my cost basis did not transfer for uncovered shares.
You cannot manually input them - I am not sure why Vanguard did not request the cost basis form as part of the transfer.
Here is the response that I got:
Our cost basis tool no longer offers the ability for you to update or enter
cost basis information for your unallocated securities. You will have to
maintain your own cost basis records for shares that we don't have cost
basis information on. We apologize for the inconvenience this may cause
Alternatively, you can contact the delivering firm and request that it
sends Vanguard a transferred cost basis statement. If we receive the
statement directly from the firm, we can allocate the noncovered shares.
The statement can be sent to us by fax at 484-582-4544 or by mail to:
Vanguard Brokerage Services
P.O. Box 1170
Valley Forge, PA 19482-1170
Hope that helps.