Q:

Twelve Labours - #11 Hesper's Hypermarket

This puzzle is part of the ‘Twelve Labours’ series, but can be solved independently.   Previous instalments can be found here: Prologue | 01 | 02 | 03 | 04 | 05 | 06 | 07 | 08 | 09 | 10

His business at the butchers’ shop completed, Hercules crossed over the road to the hypermarket to pick up some apples.   He had known the proprietor, Hesper, all of his life, and he hailed him loudly as he entered.   Hesper was sitting behind his counter, cleaning a pair of exceptionally thick spectacles, but on hearing Hercules’ voice he put them on slowly, reached for his walking stick and tottered forwards to greet him. 
“Hercules, what a relief!”  exclaimed Hesper.   “I’ve just had a delivery for the store, but those fools of a courier firm have stacked up all of my boxes totally wrong...  I mean, just look at them – it’s like they never learned to count!” 
Hercules peered into the storeroom, where forty-eight same-sized crates stood in uneven stacks against one wall.   Each of them bore a coloured label marked with a numeral, a letter or a combination of the two:

Hercules could understand why the couriers had stacked the crates in this way, grouped by their label colour – but he also knew from past experience that Hesper had his own particular way of doing things...
“How would you prefer them stacked?”  asked Hercules, keen to be helpful. 
“Why, in the right order, of course!”  hooted Hesper.   “Start with the first one and take it from there; a way to proceed will soon become apparent.   Plus, there’s a way to know if it’s done correctly – you’ll be able to spot a message I’ve left among the crates to remind myself which items are on special offer in the shop this week.   Solve it and I’ll let you take some home for your dear, sweet mother...”
Hercules paused.   “Have you ever met my mother?!”  he joked. 
TASK: Solve this enigmatic puzzle to learn which product is on special offer at the hypermarket. 
Hint 1:

 Hercules stared at the mess of crates before him, unsure of the precise arrangement to stack them in.  Hesper grinned. 

 "I suggest just laying them out in the right order first.  The precise arrangement you require will then be communicated to you somehow..."

Hint 2:

 "Okay," said Hercules, "I've laid them all out in a line in ascending order, but I'm not seeing anything." 

 "On the contrary," said Hesper. " You're seeing a coded instruction..."

A:

Very partial answer
If you

 lay out all the boxes from smallest to largest and then group them by color, from left to right, in rainbow order

you get  

 

If this is interpreted as 

 Morse code, you get: SIX ROWS

There's (at least) two ways to stack the boxes in that way, but neither way immediately gave me an answer.  I'm thinking

 Braille could be involved here, especially given the clue about Hesper's thick spectacles. 

A:

Answer:

 CUPCAKES

Building off of Jens' answer, we get the instruction

 SIX ROWS from reading each color as morse code. 

Stacking the boxes in this manner, with 1 in the lower left corner, and filling columns first yields

 

Reading this as

 Braille (since Hesper has thick glasses and presumably cannot see well), with the gray boxes as pips, yields the answer CUPCAKES.