Once you have a modded Switch, it is better to leave your SD Card in your console to prevent wear and tear on the connector, especially on HAC-001 or HAC-001(-01) models (also known as the "V1" and "V2" respectively). There are a few ways to transfer files to the Switch, both through USB or LAN.
Method 1 - USB
Hekate UMS
- Reboot into Hekate, either using the Reboot option in the power menu,
- Click
Toolson the top ribbon - Click
USB Tools - You can choose to mount your SD Card in this menu.
- Your internal system memory can also be chosen, but this is NOT RECOMMENDED under normal circumstances, and requires special software to read the data from the internal storage due to its proprietary file system, in addition to the risk of potentially bricking the console if crucial files are deleted from the internal storage.
- Plug your Switch into your PC, smart phone, or tablet, with a USB-C cable.
- Open your file manager, and you can now access the microSD card. When you're done, you can use the "Disconnect" button in Hekate to safely disconnect the two devices.
Haze MTP
Atmosphere also comes with a small application called Haze, which allows you to mount the Switch's microSD card using the Media Transfer Protocol. This is the same way smart phone storage, music player storage, or digital camera storage can be accessed over USB when connected to a computer.
Simply open the HB menu (ideally with title takeover by holding 
while booting a game) and launch the USB MTP Responder application. Once it's open, just plug the Switch into your computer with a USB-C cable, and the Switch's microSD card will show up as an MTP device.
Method 2 - FTP
Refer to the File Transfer Protocol (FTP) article for more information on using FTP software with the Switch.