I'm not familiar with My Monthly Cycles, so unfortunately I can't help you there.
In some materials I've read, they say with a 28 day cycle you should start after AF goes away. I usually wait until cd 10, but I know others begin at different times. You can BD whenever after getting a positive OPK. Some things I've read say to do it everyday, others say every other.
You should see your temperature go up for at least 3 days to indicate that you've ovulated. I know on Fertility Friend it will tell you based on your temps, OPKs, etc. when it thinks you've O'd. Typically in a pregnancy chart your temps go up and stay up....but a lot of us on here have seen some interesting charts (both pregnancy and non-pregnancy ones) so you just never know!
Best of luck!