Hello Miyamoto,
According to your application, see following advice, please!
SD3 & SD4 port can be supplied by 3.3V or 1.8V power.
---SD3 port.
From schematic of EVK, see page 6, there are 2 PINs for power input of SD3 port, one is NVCC_HIGH(3.3V), the other is NVCC_LOW(1.8V). So you can supply NVCC_SD3 with 3.3V and 1.8V at the same time, don't need to use a switch for voltage selection.
---SD4 Port
There is only one PIN for SD4 power input, NVCC_SD4, 3.3V or 1.8V can be input here. Due to only one PIN, you can use a switch to select voltage.
In my opinion, if you only use one eMMC chip on your board, better option is to connect it to SD3 port. it will make cost down(don't need a switch)
In addition, you should pay attention to Boot mode configuration, see page 339 of reference manual, BOOT_CFG2[1] is used to select voltage of SD3(3.3V or 1.8V), research page 21 of schematic, please! it can also help understand your application.
have a nice day!
TIC Weidong Sun