If you can find a 52 Hit Die corpse to animate, then I suppose you can have one big skeleton. Good luck.
Command Undead has a separate limit from animate dead, but remember that there must be undead to animate in the first place, and they get a new save every day to shrug off your control. Try not to be out of channels when that happens.
HD limit aside, animate dead allows you to make as many undead as you can touch in the same round, which according to the Magic section is six. You have to be able to touch them in the same round as the casting. I suggest piling the corpses on top of each other or laying them out in a packed row.
I don't know much about Reliquary Arms or desecrate and unfortunately don't have time to look into it right this moment. Hopefully someone else can fill you in.
Level 9 (Undead Master) now effectively level 13 raise double level HD = 26 HD. (desecrate) times 4 cleric level= 52 HD. I can raise up to 52 HD of undead…skeletons and/or zombies.
The "Undead Master" feat is poorly worded. By RAW, it does practically nothing since it only increases your caster level "when determining the number of hit dice you animate" and does not actually increase the number of undead you can control. Talk to your GM on this one.
Range or effect from Desecrate question: Desecrate has a range of 20 foot radius. It allows me to create double to amount of Undead (HD wise) because animate Dead allows me to only create one or two undead (Targets one or more corpses touched Duration instantaneous) Or does this mean I can create 1,2, 3 or 4 undead within the area?
If you are within the area of effect of the desecrate spell, then your animate dead spell is basically at double power and can create twice as many HD worth of undead. This has no effect on the maximum number you can control.
Technically speaking, the undead creature(s) you are animating doesn't even need to be inside the radius for you to gain this benefit, so long as you are (however, they will not gain the bonus hit points).
The other question about Desecrate with Reliquary Arms…the bonuses from the created undead (+6 profane bonus to negative channeled energy DCs, +2 profane bonus and +2 hit points per HD for undead created in the area) does that only apply as long as they stay within the 20 foot radius?
The profane bonuses are only within the desecrate effect, and any creature entering the area gains them. The hit points are permanent, and only affect creatures animated within the area.
Does the 52 HD level I can control only apply to the undead within the 20 foot radius of the spell as well?
Desecrate has no effect on the number of undead you control. It only affects the number of undead you can create with a single casting
of animate dead. If you can control 52 HD of undead, and you use desecrate to create a 52 HD monstrocity (good luck finding such a corpse...) then yes you can control it.It's worth noting that most of the time you'll want to create the variant "bloody skeleton", which halves the limit you can cast with a single use of "animate dead". However, that's still a maximum of 26 hit dice if you use the desecrate spell. The bloody skeleton is nice since if it is destroyed it just regenerates after an hour later. Big cost-saver. Also, always make sure you create "fast" zombies instead of the regular variety. Always nice when your minions can keep up with you.
Animate Dead is exceedingly powerful in some ways, and gives a disproportionate benefit. The problem is that all those undead that are following you around are going to cause problems for you. So it's very much a trade-off of a massive in-combat bonus for a massive headache out of combat.
Do yourself a favor and look up one of the better necromancer guides, it'll answer your questions, no need to re-hash what someone has put work into answering already.