i don't think by going into the red would encourage your club to take a loan... large loans only really exist in the game if they are already there
why don't you consider yourself the bank!!
ye you don't get the message come up on the game but, use FMRTE, put in a certain amount of money, however way you want into your balance or transfer budget etc, then make a note in the notes section of the game or separately on a note pad word document etc of the details and take it away from your club at a later date.
i can't think of any other way than doing it like that...