I'm assuming that you are using a more recent version of OJS (the following instructions wouldn't apply to versions before 2.3.0.) Also, you will want to take a look at the documentation at http://smarty.net
. OJS uses the Smarty template engine, and thankfully they keep very good documentation.
Here's how I would do things:
1. Remove the top navigation bar. you can do this easily enough by removing the line that calls the navbar template file from lib/pkp/templates/common/header.tpl:
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If you want, you don't even need to delete the line. Just comment it out.
2. Create a block plugin. All sidebar content is delivered by [url=http://pkp.sfu.ca/ojs/docs/userguide/2.3.3/journalManagementBlockPlugins.htmlblock plugins[/url]. You can move block plugins to the right or left of your page in Journal Setup Step 5, so if you make a navbar block plugin you can then move it to the left. There is information on how to make block plugins [url=http://pkp.sfu.ca/wiki/index.php/Writing_a_Block_Plugin]here[/url], and you should also look at the plugins that are in plugins/blocks/ for examples of what to do.
3. Add the navbar code to the block plugin and edit it until it looks right. Basically, just take the template code you want from templates/common/navbar.tpl and add it to the block plugin. You'll want to change some things to get it to display how you want, and you can even add more stuff in there. It should be fairly easy to do if you take a look at the smarty documentation.
You can follow these general steps to also show an issue listing of the magazine in your sidebar -- basically, create another block plugin, but this time add the code that will grab issue information (title, link to the ToC, etc.) and display it. You may want to look at templates/issue/archive.tpl, which creates the journal's Archive page, for tips on how to do this.
If you have any further questions, just let us know.