You can. Here are the steps:
I know this is an old post, but it is relevant to what I am experiencing. I installed Website Monitoring 2.6 in our development Splunk environment and I am assessing if it can do what we need for our URL monitoring. I have created a new index for the website monitoring app, and can select if from the dropdown in the setup for a URL check. I also selected the webping sourcetype manually. I created a few checkers using the defaults and one using the new index I created. When I do a search for sourcetype=webping I only see the URL checkers that are defined to the default "main" index, and no information for the checker I setup using the new index I created. I cannot even see that it ran. Any help is greatly appreciated.
Never mind on answering this. It looks like it is our development environment that is the issue and not the app.
You need to specify the index in your search or add that index to your user's list of indexes searched by default.