But I want to schedule BMD to run multiple projects in a long period of time, so that it makes bookmarking backlinks look natural and diversifies them, even these links doesn't help ranking, they shouldn't hurt either, right?
Multiple projects over a very long period is ideal. I have over 60 tasks running on one server at the moment bookmarking, each one adding a couple of links per internrnal URL a day (I set it to 35% more than I ideally want to allow for failures) It will run for maybe a month. I switch them off (pause them) when I want to run something "bigger" and more focussed for a few hours - then turn them back on again. They are all in one project folder.
My guess is the anti bot settings and email verification. Bookmarks - especially if you have a load of Pligg sites - can be a P.I.T.A. they all call to Googles anti spam servers that give them the "recaptcha" (recaptcha is Googles own anti spam solution - and Google monitor the IP's that make calls to it - you can get huge blocks of proxies banned in an hour if you have too many Pligg sites in your list)
BMD or UD (or whatever the tool is - it's the site not the tool that's causes the delay) will then stall and keep retrying to access the sign up or submit page, but finding the IP is temporarily banned.
Even across 60 running taks I only create 30 bookmarks an hour, and so UD (which is what I use) spends 75% of it's time idle - the IP ban never becomes an issue and I get 700+ bookmarks a day. I could easily pump that up to 2000 possibly even 3000 with a few more proxies added (I use 40 at the moment)
But the real reason is likely your list is out of date. Lot's of site - while still open - no longer allow sign up, and more allow sign up but then require human webmaster approval before any new account can post bookmarks - this can take weeks. You need a list with a good percentage of auto approve sites on.
Having a set up that posts 2 or 3 bookmarks a day to hundreds of URL's inside all your sites is a great way to generate a sensible amount of "social noise" (not links per se) and buying a sub from a service that does it can cost well over $100 a month depending on how many you want.
What you are trying to do is exactly right. Far better this way than some fiverr gig or 200 bookmarks to one URL a day or stupid stuff like that.
That's So "pre August 2012"
It's a good idea to have a tool that can create a couple of static URL links per URL on your sites per day in the background as well. mix up the anchor text, linking platform, have decent content where appropriate. Dont use too many directories and these days avoid "guest books" (another word for "shitty link heap") like the plague.
Big sites - or lotsa sites - best practice is continuous background dripped linking across all internal URL's (the ones that have decent content, not "tag pages" or "about us" pages and that - just your good stuff)
Roughly 50-50 split between permanent links and social noise "temporary" links like boomarks. Each URL is likely to need less than 10 in total per day - but if you've got 50 URL's or 25 websites with couple of pages each or whatever, then get a service or get automated - make sure whatever you use gives you CONTROL.
Linking without control is a short term way to the crap house.