Malignant secondary boot device.  When I plug in an external hard drive which has time machine in one partition and a secondary boot device in another, the secondary boot takes over and wipes existing files.  How do I turn it off but keep the time machine

Please help new (senior) convert to Mac Pro (OS X).  Am following the 'switching to a Mac' portable genius 2nd ed, and as it advised, I bought an external hard drive (a Mac My Word) and partitioned it with one partition for a secondary boot device and another for time machine.  Book implied I needed both.  Seemed to download OK but now when i plug in the external hard-drive it wants to reboot me fresh all over again.  How do I keep the time machine partition going but have the secondary boot device only in case of emergencies?  Do I 'eject' that partition- and if so how do I do it from outside the hard drive (I am not game to reattach it currently)

Launch the System Preferences application (under the Apple menu) and select the Startup Disk preference pane. Set your internal drive as the startup disk. Close the window.

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