No. You extract the one you do most work on to /sources and the other in /sources/phpBB3_alt. You should then have /sources/phpBB3_alt/phpBB3 although it might be a good idea to rename the one in phpBB3_alt to for example phpBB3.0, phpBB3.1 or something like that if you have more than one folder in phpBB3.
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