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>