Ať už zasadíš semínko, nebo sazenici, zalévej záhon.

It means whether ... or ..., or more loosely no matter whether ... or ....

So:

Ať už zasadíš semínko, nebo sazenici, zalévej záhon.
= Whether you plant a seed or a seedling, water the garden bed.

This is a very common Czech pattern:

ať už X, nebo Y = whether X or Y

It introduces alternatives, but the main point is that the result or instruction stays the same in either case.

This is because zasadit is a perfective verb.

In Czech, perfective verbs do not normally have a true present-tense meaning. Their present forms usually refer to the future.

So:

• zasadíš literally looks like you plant
• but really means you will plant / you plant (at some future point)

In this sentence, it works naturally as:

• whether you plant
• whether you end up planting
• whether you plant in the future

This is very normal Czech grammar.

Because the sentence is not giving two commands of equal status.

The main command is:

zalévej záhon = water the bed

The first part:

Ať už zasadíš semínko, nebo sazenici
is not really a command here. It sets up the situation:

• whether you plant a seed
• or whether you plant a seedling

So the structure is basically:

No matter which of these two things you do, do this other thing.

That is why zasadíš is used instead of an imperative.

Because Czech very often omits subject pronouns when they are clear from the verb ending.

Here, the verb form zasadíš already tells you the subject is you singular informal.

Likewise, zalévej is also clearly a singular informal command.

So Czech does not need to say ty unless it wants emphasis, contrast, or clarification.

Compare:

• Zasadíš semínko. = You will plant a seed.
• Ty zasadíš semínko. = You will plant a seed.
  This sounds more emphatic, like you in particular.

Because both nouns are direct objects, but they belong to different noun types, so their accusative singular forms look different.

1. semínko

This is a neuter noun.

• nominative singular: semínko
• accusative singular: semínko

For this kind of neuter noun, nominative and accusative are the same.

2. sazenice

This is a feminine noun.

• nominative singular: sazenice
• accusative singular: sazenici

So after zasadíš you need the accusative:

• zasadíš semínko
• zasadíš sazenici

That difference is just normal Czech case inflection.

Sazenice means a seedling, young plant, or transplant that is already growing and can be planted into the soil.

So the contrast in the sentence is:

• semínko = a seed
• sazenice = a small already-started plant / seedling

That is why the sentence contrasts two ways of starting a bed: from seed or from a young plant.

This is a question of aspect.

• zalévat = imperfective = to water, to be watering, to water repeatedly/habitually
• zalít = perfective = to water once, to give one complete watering

The imperative zalévej comes from the imperfective verb zalévat.

That often suggests:

• repeated action
• regular care
• an ongoing instruction

So here zalévej záhon sounds like:

• keep watering the bed
• make sure to water the bed
• water the bed regularly

If the speaker wanted a more one-time command, they might say:

• zalej záhon

That would sound more like:

• give the bed a watering
• water it once

Záhon means a garden bed, flower bed, or vegetable bed/plot, depending on context.

It is the prepared patch of soil where you plant things.

In this sentence, it is in the accusative singular, but because záhon is a masculine inanimate noun, the accusative singular looks the same as the nominative singular:

• nominative: záhon
• accusative: záhon

So:

• zalévej záhon = water the bed

There are two commas for structural reasons.

1. Comma before nebo

In the paired expression ať už ... nebo ..., Czech normally separates the two parts with a comma:

• ať už X, nebo Y

So:

• Ať už zasadíš semínko, nebo sazenici ...

2. Comma before the main clause

The opening part is a dependent introductory clause-like expression, and then the main instruction follows:

• Ať už zasadíš semínko, nebo sazenici,
• zalévej záhon.

So the second comma marks the end of that introductory part.

Yes, zasadit semínko is understandable and quite natural in everyday speech, especially in practical, informal language.

But you are right that Czech can also use a more specific verb:

• zasít semínko = to sow a seed

So a more specialized gardening phrasing might be:

• Ať už zaseješ semínko, nebo zasadíš sazenici, ...

However, the original sentence is perfectly normal for learners and ordinary conversation. It uses one simple verb, zasadit, for both objects.

This sentence is addressed to one person informally because of:

• zasadíš
• zalévej

For plural or formal singular/plural, Czech would use the -te forms:

Ať už zasadíte semínko, nebo sazenici, zalévejte záhon.

So:

• singular informal: zasadíš, zalévej
• plural/formal: zasadíte, zalévejte

This is a very common Czech distinction.