Dndbeyond doesn't have a way to properly put this in but I have a question. With the Ray of Sickness that it gives me, am I only able to cast it at its base level or am I able to cast it like normal but cast it at a higher level? 

Here is the ability itself:

As a devotee of Pharika, you have power over affliction. You can cast ray of sickness with this trait a number of times equal to your Wisdom modifier (minimum of once). You regain all expended uses when you finish a long rest. Wisdom is your spellcasting ability for this spell.

 It's a limited-use trait that doesn't explicitly make it available to cast with spell slots, so it would be at the base level.

Yep, lowest possible level. And this is what the SAC says about it.

What level is a spell if you cast it without a spell slot?

Such a spell is cast at its lowest possible level, which is the level that appears near the top of its description. Unless you have a special ability that says otherwise, the only way to increase the level of a spell is to expend a higher-level spell slot when you cast it.

Here are some examples:

• The warlock’s Chains of Carceri feature lets a warlock cast hold monster without using a spell slot. That casting of hold monster is, therefore, 5th level, which is the lowest possible level for that spell.
• The warlock’s Thief of Five Fates feature lets a warlock cast bane using a spell slot, which means the spell is 1st level or higher, depending on the slot that the warlock expends to cast it.
• The monk’s Disciple of the Elements feature lets the monk spend ki points, rather than a spell slot, to increase the level of a spell.

This rule is true for player characters and monsters alike, which is why the innate spellcasters in the Monster Manual must cast an innate spell at its lowest possible level.