Jeg er egentlig usikker på planen, men min chef lyder bestemt, når hun forklarer den.

Here egentlig means something like actually, really, or to be honest.

In this sentence, it adds a slightly reflective or softening tone:

• Jeg er usikker på planen = I am unsure about the plan
• Jeg er egentlig usikker på planen = I’m actually / really unsure about the plan

It often makes the statement sound a bit less abrupt and more thoughtful.

Because usikker på is the normal pattern when you are unsure about a thing.

• usikker på planen = unsure about the plan
• usikker på det = unsure about it

But om is often used when what follows is a whole clause, especially with whether/if type meaning:

• Jeg er usikker på planen = I’m unsure about the plan
• Jeg er usikker på, om planen virker = I’m unsure whether the plan works

So:

• på + noun/pronoun
• på, om + clause is also common

Planen is the definite form, meaning the plan.

Danish often uses the definite form when both speaker and listener already know which thing is being talked about. So this is not just any plan; it is a specific plan already understood in the conversation.

• en plan = a plan
• planen = the plan

Because Danish possessives work like English possessives here.

• min chef = my boss
• din bil = your car
• hans hus = his house

You do not add a separate article before the noun:

• correct: min chef
• not correct: min chefen

So the possessive already makes the noun definite enough.

Lyder bestemt means sounds firm, sounds confident, or sounds decisive.

The verb lyde means to sound in the sense of how someone or something comes across by voice or wording.

So:

• Hun lyder bestemt = She sounds firm/confident

This is different from:

• Hun er bestemt = She is firm/determined as a person
• Hun taler bestemt = She speaks firmly

So the sentence is about the impression her voice/explanation gives, not directly stating a permanent personality trait.

Here bestemt means something like:

• firm
• confident
• decisive
• certain

It does not mean definite here, even though that is another possible meaning of bestemt in other contexts.

For example:

• en bestemt plan = a specific/certain plan
• hun lyder bestemt = she sounds firm/confident

So the meaning depends a lot on context.

Because når is used for when in general, repeated, habitual, or present/future situations.

Here the meaning is something like:

• when(ever) she explains it
• when she is explaining it

By contrast, da is usually used for a single past event:

• Da hun forklarede den i går, lød hun bestemt = When she explained it yesterday, she sounded firm

So in your sentence, når fits because it sounds general or habitual, not like one specific past moment.

Because after når, you have a subordinate clause, and Danish subordinate clauses do not use normal main-clause V2 word order.

Main clause:

• Min chef lyder bestemt
  Verb comes early, as expected in Danish main clauses.

Subordinate clause:

• når hun forklarer den
  hun comes before forklarer

So this is the normal pattern:

• når + subject + verb

If you are used to Danish main-clause inversion, this difference is very important.

Because den refers back to planen, and plan is a common gender noun:

• en plan
• therefore: den

If the noun were neuter, you would use det:

• et forslag = a proposal
• Jeg forstår forslaget, når hun forklarer det = I understand the proposal when she explains it

So the pronoun must match the gender of the noun it refers to.

Yes, egentlig is fairly movable, but the nuance can shift slightly.

Your version:

• Jeg er egentlig usikker på planen
  Very natural. The focus is on being actually/really unsure.

Other possibilities:

• Egentlig er jeg usikker på planen
  More marked; it can sound like actually, I’m unsure about the plan.
• Jeg er usikker på planen egentlig
  Usually less natural in this context.

So the placement in your sentence is a very standard and natural one.

The comma before men is standard because men joins two clauses:

• Jeg er egentlig usikker på planen
• min chef lyder bestemt

The comma before når depends on comma style. Many written Danish texts include it, especially with start comma style:

• ..., når hun forklarer den

So:

• comma before men = normal and expected
• comma before når = also common, depending on comma convention

In any case, the sentence as written looks completely natural.