You can access your Ledger transactions by adding the actual blockchain as a wallet and entering your Ledger’s address for the relevant currency. Give the wallet a name something like “ETH & Tokens (Ledger)”. For BTC which uses multiple addresses you need to add them all with a comma between each one. Every time you generate a new address in future you will need to remember to update the Koinly wallet with the new address, otherwise the transaction will show up as a withdrawal rather than a wallet transfer.
You can use the xpub address which can be found in the Ledger. This is the master address for BTC from which all the BTC addresses that the Ledger generates are derived. Koinly can then import transactions for all the BTC addresses it generates and you do not have to update with the new address as they are created.
Some other cryptos like LTC also use xpub address but not all. Also make sure that Koinly supports them to.
I think it is a privacy issue, in that anyone knowing your xpub means they can see your activity regardless which actual address is used…but then that is exactly what you want koinly to be able to do so probably not much to worry about.
Also would like to see integration with LedgerX. I see they now have API Keys available so it seems like an integration would be straightforward hopefully.