There's no way to control when indexing will occur but Windows is usually quite clever about not overloading your system while you're using it. Once the initial index is finished the overhead should be minimal.
There are other search products that do allow you to specify when an index is built but I can't think of any that are free. If you're only searching by file name then look for an NTFS-MFT based search tool (like NTFS-Search) which can search file names in seconds.