aren't payments in lightning split (or can be split)?

Assuming Alice and Bob wants to make use of lightning network, Bod is the owner of one coffee shop, Alice is the customer. Both of them will have to open a channel, the channel is just a 2-of-2 multisig, which means both of them will have the knowledge the transfer of any particular amount they both agreed upon.

If they both agree to put 0.005 btc each on the channel

Alice: 0.005 btc
Bod: 0.005 btc

That means they both have 0.005 btc + 0.005 btc = 0.01 btc on the channel. Assuming Alice went to Bob's shop for coffee and he or she paid 0.0001 btc, the money will be deducted from Alice btc to Bob Btc on the channel. Which means Alice will have 0.0049 btc as 0.0001 btc is transferred by her on the channel while Bob will have 0.0051 btc for the coffee Alice paid for and so on until anyone of them closes the channel.