If your application has custom classes and is deployed as a runnable jar and not contained within the spring batch admin, you cannot start jobs. You can only view the status of jobs and "kill" their status in the database.
If you look at http://static.springsource.org/spring-batch-admin/reference/reference.xhtml at the end of the Configuration Upload section it states
You can see a new entry in the job registry ("test-job") which is
launchable in-process because the application has a reference to the
Job. (Jobs which are not launchable were executed out of process, but
used the same database for its JobRepository, so they show up with
their executions in the UI.)
If your jobs are strictly configurable jobs, as-in you use only XML to define them and do not need to do any customized item readers/processors/writers or other custom classes, then you can upload the job XML and it will be runnable from within the admin site. If you have custom classes then, from my experience, you will have to have the spring batch application deployed within your web application and then upload an XML that contains the jobs you want to run separately.
I personally just used the Admin tool to view job status and provide me with statistics through some custom pages. I left the scheduler to run the jobs and I didn't want those with access to the admin site to kick off a job when they knew nothing about it. Basically, used it to give the users a warm fuzzy without allowing them to muck it up. (leave it to a user to find an edge case you didn't account for)