If you want separate windows within the same instance of excel, you can try:
Tools|Options|View tab|Show section|Check Windows in Taskbar
If you really want separate instances of excel...
If you use File|Open within excel, then each of these workbooks will be open in
the same instance of excel. This won't work for you.
If you open the file via doubleclicking in windows explorer:
You can change this setting:
Tools|Options|General tab|Ignore other applications (check it)
Be aware that one side effect of having this setting checked is sometimes you
can't open a file by double clicking on it in explorer. (toggle it back and
that should be fixed.)
This shows up for workbooks that have spaces in their name or path:
c:\my documents\excel\testworkbook.xls
or
c:\test of workbook2.xls
Cannot find C:\my, then more "Cannot find ..." messages.
It's more trouble than it's worth (for me, anyway).
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If you're using multiple monitors, you may want to review Chip Pearson's notes:
http://cpearson.com/excel/MultipleMonitors.aspx