Where other than Kronstadt did the Russian American Company train its employees?

I think there's been a misunderstanding somewhere. General schooling and navigation are very different beasts.

Navigation

Navigation would have been primarily studied at sea; formal navigation schools were not common until well into the 19th century though there are early examples (Gardes de la Marine). The first naval school in Russia was the Advanced Officers' Class, instigated in 1827. The primary method for learning navigation before this would have been at sea though (see below) some land-based teaching was also done for this in Novo-Arkhangelsk.

As other civil examples, the Admiral Makarov State University traces its beginning to 1809 when it was founded as the Corps of Engineers for Hinterland and Waterway Transportation. Their focus was very much on land routes and transportation, and they were reformed into the Corps of Railway Engineers in 1810 and it stayed this until 1864.

The Maritime State University describes the development of merchant seamen's education with 1876 as the first organized curriculum in the Russian East, then located in Vladivostok. This is already after the (effective) demise of the Russian–American Company in 1867.

General Schools

Civil administrators had their own schools, but even these come about relatively late. For example, the Imperial School of Jurisprudence was founded in 1835. The RAC did, however, have local schools with an orientation on trades (i.e., the most useful thing for the RAC). Wikipedia's listing of the RAC's outposts might not include all locations, but that was my guide.

• Fort Ross didn't have a school as no descriptions of the site mention one;
• The Hawaiian forts (Alexander, Barclay-de-Tolly, and Elizabeth) didn't have schools;
• Kodiak Island (Pavlovskaya) had a school shortly after 1784 (quote below);
• Novo-Arkhangelsk had schools (quote below):

Grigor Shelikof is usually credited with establishing the first settlement on Kodiak Island in 1784 and the first school shortly thereafter. When the Russian-American Company was given monopoly rights over the Alaska trade and was vested with governmental authority, it was required to establish and maintain schools. In addition to the Company schools, missionaries of the Greek Church also established schools with religious teaching as their main purpose. The Russian-American Company was anxious to train youths for its service, and a school was started in 1805 for this purpose. At Sitka, the Russian commercial center, a school was opened in the same year. After 15 years of a rather unstable existence, it was taken over by a young naval officer, who conducted an efficient school for 13 years. In 1833 it was further improved by the patronage of Etolin, a Creole who had become director of the Russian-American Company and Governor of the colony.

Another school was soon started in Sitka for the sons of workmen and employees of the Company. Mechanical trades and religion were taught in order that the best of the pupils could be trained to enter the Navy or the priesthood. There was also a girls' school which offered sewing and household work in addition to Russian, reading, writing, and arithmetic. A theological school followed, which grew into a seminary by 1845. The curriculum was composed of Russian, religion, navigation, trigonometry, geometry, geography, history, arithmetic, bookkeeping, and English. In 1860 a general colonial school was opened in accordance with the ukase of the preceding year. Of the twelve pupils enrolled, eight were to be educated for Company service, and four were the sons of Russian priests.
_{—'Contributions to Education'}

• Unalaska had a school from 1826 (built by Veniaminov):

Veniaminov designed and built the Church of the Holy Ascension, along with his own home and a school in 1826. He and his wife taught in the school, which had about a hundred pupils of both genders, instructing them in scholastic subjects and trades. This education, like all assistance to Native Alaskans, did not come without a price, however. All men educated in company schools were obligated to serve the Russian American Company for ten to fifteen years.
_{—'Encyclopedia of American Indian History'}

These are the only ones I've been able to confirm (and the negatives about Forts Ross, Alexander, Barclay-de-Tolly, and Elizabeth I'm also quite sure about).