Your question is a little vague....
I think you meant:
" would automated
SEO software will hurt my site like bookmarking and article submission"
Using automated software as part of your efforts to rank your website (making SEO) will not hurt your website if you do it the right way.....
As gregstereo said to must get slow at first....
But before you make any move about this you must look at the onsite SEO and content... after you sure the you done everything about onsite you can move to the offsite SEO... I say that, because if google start discover backlinks to your website and go to your site and see that is a mess you will get in trouble....
After this you can move to the offpage SEO and use automated software to create backlinks, any kind o backlinks. As already said you must use good and proved software that make their reputation in time...
Second you must go slow in building backlinks and alternate your combination, all trough I manage to rank first page on a 11 mil searches building most blog comments (most meaning 90%) .
Before start using this software read, watch and learn as much as you can... there are many tutorials out there... for free... In my opinion is not worth to spend your money on ebook or thing like this... use google...
And finally I will say you another thing.... If an software can get an website been banned why you do not find anyone use it to destroy the competition? What will stop me to blast my competition websites with 100k or 1 mil of backlinks to get the out of the way?... I tell you what... If I will do that it is possible to see them lose some position or pages but after a while they will rise stronger and higher....
So go for it... use software but... make your research before... and study...
Good look and if any help need it feel free to contact me or ask around here...
I use software.....