When you add the html editor instance to the page, it will add a line similar to:
$CKEditor_config["filebrowserBrowseUrl"] = "webassist/kfm/index.php?uicolor=".urlencode(isset($CKEditor_config["uiColor"])?str_replace("#","#",$CKEditor_config["uiColor"]):"#eee")."&theme=webassist_v2&showsidebar=false&startup_folder=folder1";
the last argument:
&startup_folder=folder1
set the subfolder of the main upload folder that the instance will use, in my example case, I set the upload folder in site settings to use "uploads", this will set the editor to use the uploads/folder1 directory for this instance.