Time machine backup to my External Drive ...

Hello,

Your best bet would be to clone your whole drive to a new Partition on the external drive, but repartitioning is not without risk.

TM should work though not ideal.TM only backs up the account your in as I recall.

Whatever you do be sure to Safe Boot, holding SHIFT key at bootup to repair the boot drive, then use Disk Utilityto Repair Disk on the external drive.

To answer your questions about Time Machine, ideally, you should have an external drive that is dedicated for your Time Machine archive. Then, back up BOTH your MacBook's internal drive AND that external drive with user data, to your sufficiently large Time Machine drive. Time Machine backs up your entire internal startup disk volume (all user accounts) and other connected volumes that you do not exclude. External drives are excluded from the backup by default, but you can set it to NOT exclude them. And you can set it to exclude specific folders that you do not want to back up. For example, I exclude my Downloads folder, because I consider those files (such as software installers) to be "temp" files that I can re-download, and if I want to keep something that I downloaded, I move it to a place that IS backed up by Time Machine.

However, using Time Machine does not erase existing data on the external drive used for its archive. The Time Machine archive is placed in a folder called Backups.backupdb. Your existing data is not effected, but it's not backed up either (Time Machine does not back up data on its archive drive). You should set it up and try it, to see for yourself how Time Machines stores its archive data.

You can use your Time Machine archive as your data source, if you need to restore your user data after upgrading to El Capitan. You can either do it manually, by using Finder to copy data from the archive to the appropriate locations on your new system. Or use it with an automated process, like Migration Assistant, and migrate from the Time Machine archive.

Going from 10.6.8 to the latest OS X is a large jump. Some of your existing third-party apps (especially older apps that have not been updated) may not be compatible under El Capitan. If you find that you need to go back to your previous system, you can do so from your Time Machine archive. To do this (with Snow Leopard), you start up from your Snow Leopard installation disc. When you get to the installation screen (after selecting language), look under Utilities (in the menu bar) for Restore From Backup. This utility lets you select the Time Machine backup state to use to do a complete restore. Since Time Machine backs up incrementally (every hour it is active), find the backup state immediately before you installed the El Capitan upgrade.

Before upgrading to El Capitan, try starting up from the Snow Leopard installation disc so you know where to look. Don't actually do it, but be familiar with how to get to that point. You can cancel out and restart normally.

Also, if you don't have Time Machine running all the time, be sure to have it do one last backup under Snow Leopard before doing the El Capitan upgrade.