yes of course you can. For remote views Options=>Media Network=>Advanced= customize views ...Remember, until they decide to combine the three, there are 3 separate areas for your views. Theater and Remote Modes can even import views from Standard mode (including your custom views). Most functions "port" over (some do not or are available only for Theater and Remote Modes). Just click the add button.Then library item from Standard View if you want to incorporate veiws you have already made.
I personally don't use any of the out-of-the-box views. Your choice, you can delete them (they can be reloaded so no worries)
BTW, they will not show up immediately in JRemote. Disconnect and/or reboot JRemote in your ipad/device - then reconnect. You should then see the changes you made.