Dear GiJOE,
I've installed ALTSYS...
It's far better, if you want to play with templates(and not only)!
Now, regarding smartfaq (and smartsection as well) I have the same issues.
I found the following chank of code
<div style="text-align: center; padding: 3px; margin:3px;">
<{$commentsnav}>
<{$lang_notice}>
</div>
<div style="margin:3px; padding: 3px;">
<!-- start comments loop -->
<{if $comment_mode == "flat"}>
<{include file="db:system_comments_flat.html"}>
<{elseif $comment_mode == "thread"}>
<{include file="db:system_comments_thread.html"}>
<{elseif $comment_mode == "nest"}>
<{include file="db:system_comments_nest.html"}>
<{/if}>
<!-- end comments loop -->
</div>
and I replaced it with
<{d3forum_comment dirname=d3forum forum_id=(number) itemname="id" subject=$title}>
on both modules.
The result is that the oldfashion comment system disappeared from the bottom of the item (since I remove the correspoding code) but nothing comes up in this place.
I've did the comment integration with pd-downloads with success.
I'll keep investigate it...