Hello,
If you uses LabVIEW or LabWindows/CVI IDEs the best way to control your instrument is to use the instrument drivers provided on our site:
http://search.ni.com/query.html?lk=1&col=alldocs&nh=500&rf=3&ql=&pw=595&qp=%2BContentType%3AInstrumentDriver&qt=HP+54111&layout=IDNet
If for some reason you must use GPIB commands the best for you is to request from HP the set of commands for your scope.
I assume that you have some commands for configuration of your scope then you can enable ch1 and ch 2. then when you acquire data your scope will probablely fill a memory buffer (record) with your signals data. so i think that there is only one function for one channel and two channel. When using two channel tha data will probably be interleaved in your record i
.e (ch1[0],ch2[0],...ch1[n],ch2[n]) .
Hopes this helps
Regards
Salissou ISSA
Applications Engineer
NI France