The record company will not take it out of your concert/t-shirt money unless you've signed away all your revenue streams and/or soul to your label like Robbie Williams did with EMI. Generally when you sign a record deal, your advance will be recoupable (i.e. a loan against your cut of future earnings) and your recording costs may or may not be depending on your leverage and your lawyer.
e.g. Your first record costs £$â50k to produce and both it and your 50k advance are recoupable. Your cut of record sales for the first year is 80k, therefore you don't earn any money until the next year once the money you're due reaches 100k. Recording costs in many cases are not recoupable so in that case you'd be 30k up.
Generally record labels only own the physical recordings and right to licence them! In most cases they have no right to your earnings from mechanical royalties, sync fees (from songwriting in both cases), touring or merchandise!