I would reccommend NOT leaving toys or bones for your pup while you are gone, as the vast majority of them should only be used under supervision--same as with kids. If you have to leave a toy while you're gone, the most 'safe' toy to leave would be the thick rubber toys, if anything. In addition, I would only leave water out for your pup during the day as long as you are there in the morning and evening to feed. I do not believe that leaving dog food out for them to chomp on at their leisure through the day is the best way to feed. Please refer to the attached link for detailed information about the dangers of particular dog toys, bones, rawhides, etc.
DOGTOYS.doc
In addition, when you are home on your days off, put the pup in the crate for 15 minutes or so once or twice throughout the day for crate time. Be sure to estatically praise him/her when he/she goes in and afterwards when he/she comes out, so that he/she realizes that going into the crate is nothing to be afraid of.