As long as the version number is different (which is required), you can specify the correct version through the web.config file. This is how I have settings in one of my applications to link to the correct version of Crystal Reports, since we have several versions in the GAC:
<system.web>
<compilation>
<assemblies>
<add assembly="CrystalDecisions.Web, Version=11.5.3700.0, Culture=neutral, PublicKeyToken=692FBEA5521E1304"/>
<add assembly="CrystalDecisions.Shared, Version=11.5.3700.0, Culture=neutral, PublicKeyToken=692FBEA5521E1304"/>
<add assembly="CrystalDecisions.ReportSource, Version=11.5.3700.0, Culture=neutral, PublicKeyToken=692FBEA5521E1304"/>
<add assembly="CrystalDecisions.Enterprise.Framework, Version=11.5.3300.0, Culture=neutral, PublicKeyToken=692FBEA5521E1304"/>
</assemblies>
</compilation>
</system.web>
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