Peter here from Shopify Support!
If by "store" your funds, you're referring to how Paypal keeps your funds within your Paypal account until withdrawn, then no, Shopify Payments wouldn't store your funds. When using Shopify Payments, our fee will automatically be deducted from the amount, then sent to the banks for processing. Once the banks have processed the payout (this length of time depends on the country you reside in), the money will be deposited into your bank account.
If this doesn't answer your question, or if you have any other questions feel free to reply back here and I'll happily help out!
All the best,