ny bank account not compatable to be linked with my Demat... help

i am opening a online Demat account in sharekhan ,..
my present bank account can't be linked withe the Demat account,now i am left with the option of opening another bank acount in the compatable bank ( which i dont want ) ,or do the transacions through cheques ...

what difference will it make ..if i do the transactions through cheques...
i will be trading with the fixed amount of money say 10k or 5k in starting.

as i am a starter,
any advise in selecting Demat,brokerage rate,and other think to keep in mind while selecting Demat would be very valuable

Thank YOu