As you know when you instal Ontolica on a Moss box it overrides the default sharepoint delegate search control with ID "SmallSearchInputBox", this is the searchbox that we are customising below.
To customise ontolica search, i.e. to change the search magnifying image button or to change the css classes you just need to modify the xslt file that ontolica uses.
This can be found in the location RootSite/OntolicaStyles/Forms/Allitems.aspx and open the folder SearchBox and edit the default.xslt file in here...you can change the images, change the borders around the search boxes etc.
You do not need to do an IISRESET but it seems to take a while before the changes are reflected on the page so if it is a dev box do an IISRESET to see the changes immediately.