In a capitalistic world... you are free to charge whatever you want to charge. It makes no difference if you charge 100%, 200%, 500%, or 1000% more than any printing costs.
The only thing which matters is... what will clients be willing to pay.
That being posted, I would always charge a markup on any carried costs. If printing costs X, then I would charge X+(X*0.2) for printing (20% markup) as a minimum for printing.
It can also be wise to require printing costs be paid in advance, especially for large printing bills. The last thing you want is a client sticking you with a printing invoice for a lot of money.
Design fees would be above and beyond any printing fees.
So, for example...
If printing costs $500 + $50 for shipping
You intend to charge $600 for design
The total project cost is $1,260, landed
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(550 + (550*.2)) + 600 = 1260
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And a $660 (non-refundable) deposit is required before printing is done (if not sooner).