I am trying to install 5 sound sets/banks on my MX61v2 and it's more than a bit confusing.

There is room for 128 Normal User Voices, 8 Drum User Voices, and 128 (16-Part) Performances in your MX61. Each of the listed numbers is the maximum. Attempting to install 5 sound sets can be handled by loading them one at a time. Loading one will replace the other.

A sound set like “Bomba Latina MX SoundSet - LATINAMX61.X5A (31 Performances / 23 User Voices)” will occupy 31 of the possible 128 Performance locations. Many of those Performances utilize the 23 Normal Use Voices they included in that set.

All Performance locations are USER locations and each Performance can contain 16 Voices. The Voices are recalled from the 1106 factory Preset Normal, 61 Preset Drum Voices, and the 128 User and 8 User Drum Voice locations.

MX BASICS
A Performance can contain 16 Parts. Each Part contains one Voice.
Parts 1 and 2 can be “linked”... this means they both will be accessible via the Keyboard together....
__ You do so by pressing either the [LAYER] button — which maps the Part 1 and Part 2 sounds across all keys...
Or you can press the [SPLIT] button — which maps the Part 1 sound from the Split Point and above, the Part 2 sound is mapped below the Split Point.

When you talk about the two Voice Names in the screen... the upper one is Part 1, the one on the bottom is Part 2.
When you play the arrow icon in the screen indicates which one is sounding.
Use the Down Cursor to move between Part 1 and Part 2
You could also press [PART SELECT] then press button [1] or [2]

When you [LAYER] these two Parts, they can be named and stored as a User Performance.

To play through the factory 128 Performances:
Press the [SELECT]
This places you in Performance mode.
The screen will read “Performance Select” on the top line, and the Performance Name on the bottom “001 (A01) MX Category”

There are 128 Performances
The Group is designated by a capital letter A-H, the program within the Group is designated by a number 01-16.

Hold [SHIFT] + [INC/YES] to move to Group B, There are sixteen more Performances in this Group 01-16

The Performances can be either a Layer or a Split (utilizing Parts 1 and 2) — additionally, a Rhythm Part (DrumKit in Part 10) may be added to your Layer or Split. The Drum Kit Part is linked to a Drum Pattern that can be used to accompany you playing the Layer or Split.

1. What the heck??? I'm sure someone else has been through this. Is this an editor issue that you have to save all of your user voice presets as you go and then be able to add them at the end?

A few rounds with the Manuals will help with the navigation and basic operations. When loading data from a .X5A file you can select to load “All” data, “All without System” or you can select to load “Performances”... see pages 61 and 62 of your Reference Manual (pdf). This will step you through selecting a Source (Src) Performance, a Destination (Dst) Performance location - yes you will be overwriting a location in order to load this Performance.

2.How do you set the boot to remember the last voices you had pulled up?

You can have the MX power on with any of the 128 Performances. You do so by setting the “StartUp” setting.
Press [UTILITY] > select “General” > scroll though the parameters - near the end, find “StartUp” select the Performance by number 001-128

3. Can someone please tell me if I'm suppose to install both files the MXVISY.X5A & MXVISYNF.X5A? I don't have an iPad so I don't have access to the FM app. I've been reading info on this install and it's confusing well. I've been loading MXVISYNF.X5A.

As mentioned, if you set the LOAD option to “All” - then loading a file will replace ALL data

(FILE MXVISYNF.X5A)
The Performances of this set solely use Voices of the MX 49/61 V2. The first part of these Performances (001 to 032) has been programmed to correspond approximately to the counterpart of the Bank in FM Essential in order to use this set without an iOS device.

See article on page 12: Music Production Guide 09/2016 (pdf)