You're really looking to combine two themes into one (or to partially combine two themes). You can't do this just with the themeroller, but you could extract the relevant parts of your custom theme and add #top
to the selectors. So where the generated theme might have
.ui-state-default a, .ui-state-default a:link, .ui-state-default a:visited {
...
You'd edit it to be
#top .ui-state-default a, #top .ui-state-default a:link, #top .ui-state-default a:visited {
...
Potentially a lot of work and not very efficient, but the way jQuery UI themes are set up, they apply the same styling to all the elements