Gosh its been years since raising a pup and im stuck

So far so good with the crate training considering i have never crated any other of my dogs, i am only doing it this time because the last dog i had wrecked my whole house i put her in it at night and she eats in it and takes herself in it during the day at times apart from that she has a free run around the place with me. i feel so bad though cause last night she messed in it so im guessing thats my fault i maybe didnt get up in time?? i had made sure she went toilet before putting her in there? im paper training her for now until i move in a few weeks where ill have a garden at present im in a flat.
do i ignore the whining when i first put her in there at night? she doesnt whine through the day? and in 2 weeks i will have to leave her in the crate while i do the school runs? also she seems to want to play very rough as in biting me or grabbing ankles etc... i just replace with toys? she is very young (6.5 weeks) rottie cross bullmastiff my last rottie was very different in comparison and i had him from 7 weeks however i know no 2 dogs are ever the same. any advice will be appreciated