What you need to do is merge your library config sections to app.connfig. Merging config files is done by first adding elements inside the <configSections> config element, to identity the config section and then by adding the config elements inside the configuration element.
Example of merging config files:
App config:
<?xml version="1.0" encoding="utf-8" ?>
<configuration>
<configSections>
<sectionGroup name="userSettings" type="System.Configuration.UserSettingsGroup, System, Version=2.0.0.0, Culture=neutral, PublicKeyToken=b77a5c561934e089" >
<section name="CA3.Settings" type="System.Configuration.ClientSettingsSection, System, Version=2.0.0.0, Culture=neutral, PublicKeyToken=b77a5c561934e089" allowExeDefinition="MachineToLocalUser" requirePermission="false" />
</sectionGroup>
</configSections>
<userSettings>
<CA3.Settings>
<setting name="Setting" serializeAs="String">
<value>2</value>
</setting>
</CA3.Settings>
</userSettings>
</configuration>
Library config:
<?xml version="1.0" encoding="utf-8" ?>
<configuration>
<configSections>
<sectionGroup name="userSettings" type="System.Configuration.UserSettingsGroup, System, Version=2.0.0.0, Culture=neutral, PublicKeyToken=b77a5c561934e089" >
<section name="CA3.Library" type="System.Configuration.ClientSettingsSection, System, Version=2.0.0.0, Culture=neutral, PublicKeyToken=b77a5c561934e089" allowExeDefinition="MachineToLocalUser" requirePermission="false" />
</sectionGroup>
</configSections>
<userSettings>
<CA3.Library>
<setting name="Setting" serializeAs="String">
<value>1</value>
</setting>
</CA3.Library>
</userSettings>
</configuration>
Merged app.config containing both library and app configuration.
<?xml version="1.0" encoding="utf-8" ?>
<configuration>
<configSections>
<sectionGroup name="userSettings" type="System.Configuration.UserSettingsGroup, System, Version=2.0.0.0, Culture=neutral, PublicKeyToken=b77a5c561934e089" >
<section name="CA3.Settings" type="System.Configuration.ClientSettingsSection, System, Version=2.0.0.0, Culture=neutral, PublicKeyToken=b77a5c561934e089" allowExeDefinition="MachineToLocalUser" requirePermission="false" />
<section name="CA3.Library" type="System.Configuration.ClientSettingsSection, System, Version=2.0.0.0, Culture=neutral, PublicKeyToken=b77a5c561934e089" allowExeDefinition="MachineToLocalUser" requirePermission="false" />
</sectionGroup>
</configSections>
<userSettings>
<CA3.Settings>
<setting name="Setting" serializeAs="String">
<value>2</value>
</setting>
</CA3.Settings>
<CA3.Library>
<setting name="Setting" serializeAs="String">
<value>1</value>
</setting>
</CA3.Library>
</userSettings>
</configuration>