The Movable Type documentation does not really explain this well in its example. I've only gotten this far into getting/setting MT::PluginSettings objects because that's all that I've had to do so far, but this is a start to explain how to get it done right. I ran into a problem where the default scope setting of "blog" for the get_config_value method of MT::Plugin was not retrieving the value for the plugin-in for a particular blog, relying instead on the default value of 0. In the getter code, I did the following:

sub editBlogPolicies
{
    my $plugin = shift;
    my $app = shift;
    my $template = $plugin->load_tmpl("blog_policy_editor.tmpl");
    my $obj_type = $app->param('obj_type');
    my $obj_id = $app->param('obj_id');
    my $blog_id = $app->param('blog_id');

    my $iter;
   
    MT->log({message => $plugin->get_config_value("include_entries", "blog:1")});

    if ($plugin->get_config_value("include_entries", "blog:$blog_id") == 1)

The MT::PluginSettings was built up like this:

my $plugin = MT::Plugin::BlogPolicy->new({
    id        =>    'blogpolicy',
    key        =>    'mt-blogpolicy',
    name        =>    'Blog Policy Link Plug-in',
    description    =>    'A plugin for organizing links to site policies.',
    version        =>    $VERSION,
    author_name    =>    'Moi, non vouz',
    schema_version    =>    $SCHEMA_VERSION,
    blog_config_template    =>    'config.tmpl',
    settings => new MT::PluginSettings([
            ['include_entries', {Default=>0, Scope=>'blog'}]
            ])
});

The config.tmpl file looks like this:

<mtapp:setting
    id="include_entries_setting"
    label="Choose from entries and pages"
        hint="<__trans phrase="By default, the plug-in only allows you to choose pages.">"
        show_hint="1">
        <input type="checkbox" name="include_entries" value="1"
        id="include_entries" <mt:if name="include_entries">checked="true"</mt:if>/>
</mtapp:setting>

The key is to make sure that you use the  form blog:$idnumber to get the correct setting, as shown in bold above.

I know the examples may seem a bit gratuitous, but most of my coding done at work is in Java, which makes me pine for good, detailed, example-rich documentation. Better to provide too little example, than too little, in my opinion.