Packing and shuffling tokens is a common practice in training auto-regressive language models to prevent overfitting and improve efficiency. Documents are typically concatenated to chunks of maximum sequence length (MSL) and shuffled in chunks of tokens (atom-size chunk), possibly breaking context within documents. An alternative approach is padding, which only includes one document per chunk. To optimize both packing strategies (concatenation vs padding), we explored the optimal atom size for shuffling and compared performance and efficiency. We found that in the most common setup (where average document length is greater than MSL), matching atom size to MSL yields the lowest perplexity, controlling for dataset. Also, padding yields lower final perplexity than concatenation at the cost of lower efficiency. This trade-off informs the choice of shuffling and packing methods in training LMs.