Leevi,
Finally gave your plugin a shot. Initially, I was having trouble uploading to a directory, but once I switched it to another one, I logged in through FTP and found the files there. 
Problem is, when I went to “Edit” and checked out the entries, the custom field I used for the file was not updated and was left blank.
I used this code for the SAEF, pretty much what you supplied in your initial post.
{exp:weblog:entry_form weblog="upload" lg_saef_file_upload="y" lg_saef_file_upload_dir_id="3"}
<p><input type="text" name="title" id="title" value="{title}" /></p>
<div>
<input type="file" name="field_id_12" value="" />
</div>
<input type='submit' value='submit' />
{/exp:weblog:entry_form}
If it’s any consolation, I’m running ExpressionEngine 1.6.4.. Fields are uploading, just the field isn’t populated when I hit “Edit”.
Just to be clear on how this works.. I created a custom weblog field and made the the field type “Text Input” and popped a 384 character limit on it. After it’s created, I check the field_id for the designated field and apply that to the “name” of the field in an SAEF? Also, just inacse you need to know, I just updated to the newest version of EE and am attempting this upload as a Super Admin.
Cheers,
Danny