If the CLEO where you are stationed won't sign off, your best bet is to wait until you are home. If a CLEO will sign, his shop will probably do the prints.
Make sure you they the ATF "applicant" fingerprint cards (light blue). ATF sends them to the FBI to run the prints and if they are not ATF cards they can go astray and delay things (even more than usual) or even require resubmission.
As to multiple applications, AFAIK there is no limiit, but I have never submitted more than one so I don't know if you need two cards for each application or if one set will do for all. The instructions should tell you, but FWIW, I think it would be best to submit a set for each application, in case the applications get separated. I know you have to submit a set of photos for each application.
Jim
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