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when I type the url of most of my catetory pages in the G search box
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Usually, its harder to get deeper pages indexed than the home page simply due to lack of PageRank. If you have a ton of outbound links on every page (especially the home page), your site gives away too much juice to other sites instead of pumping that juice to internal pages.
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Perhaps I should just wait a while..? I mean after they are indexed, should I allow for a certain amount of time before they show up in the search?
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Yeah, usually Google will get around to indexing pages sooner or later. How quickly your pages get picked depends mostly on PageRank, but it also depends on other factors, like how often you update your site.