This is how you flash to eMMC easily

[wibble]

The eMMC is the first block device, and the uSD the second. Either may contain partitions which the GUI may show as drives to mount. dmesg will show the details, something along the lines of:

[178118.500549] scsi 4:0:0:0: Direct-Access JumpDriv e eMMC PQ: 0 ANSI: 2
[178118.500800] scsi 4:0:0:1: Direct-Access JumpDriv e microSD PQ: 0 ANSI: 2
[178118.503076] sd 4:0:0:0: Attached scsi generic sg2 type 0
[178118.506159] sd 4:0:0:1: Attached scsi generic sg3 type 0
[178118.506302] sd 4:0:0:0: Power-on or device reset occurred
[178118.507808] sd 4:0:0:1: Power-on or device reset occurred
[178118.508154] sd 4:0:0:0: [sdc] 30785536 512-byte logical blocks: (15.8 GB/14.7 GiB)
[178118.508263] sd 4:0:0:1: [sdd] 249737216 512-byte logical blocks: (128 GB/119 GiB)
[178118.508511] sd 4:0:0:1: [sdd] Write Protect is off
[178118.508513] sd 4:0:0:1: [sdd] Mode Sense: 0f 00 00 00
[178118.508636] sd 4:0:0:1: [sdd] Write cache: enabled, read cache: enabled, doesn't support DPO or FUA
[178118.509335] sd 4:0:0:0: [sdc] Write Protect is off
[178118.509336] sd 4:0:0:0: [sdc] Mode Sense: 0f 00 00 00
[178118.509529] sd 4:0:0:0: [sdc] Write cache: enabled, read cache: enabled, doesn't support DPO or FUA
[178118.514637] sdd: sdd1
[178118.519379] sdc: sdc1 sdc2
[178118.520597] sd 4:0:0:0: [sdc] Attached SCSI removable disk
[178118.520714] sd 4:0:0:1: [sdd] Attached SCSI removable disk

Generally when you're flashing you target the underlying drive, not the partition, so in this example /dev/sdc is the eMMC and /dev/sdd is the uSD card.