Because I have studied Estonian history and I am Estonian myself, I can mainly give an answer about the situation in Estonia.

As far as their numbers go, Baltic-Germans were never very numerous. According to the Russian Empire Census there were only 180,000 Baltic Germans in Russia's Baltic provinces (moderen day Estonia and Latvia (except Latgale region)). In comparison at that time (1897) population of those provinces was arround 2,4 million. That means that Germans weren't there in high-numbers.

While Germans weren't very numerous, they had control over most cities. During that timeline (16th-19th century) most prominent cities in modern-day Estonia (Tallinn, Tartu, Pärnu, Viljandi, Narva) still followed Hanseatic laws. That meant that city officials were chosen up until early 19th century only amongst the German merchants. That meant that city was run by Germans and was mainly meant for Germans. That of course attracted Germans from countryside and from abroad. Until industrialisation took place in early 19th century most cities had German or sometimes Scandinavian high-end crafters (bakers, goldsmith, shoemakers etc) and merchants, while most Estonians worked as less valued crafters (f.e builders, butchers, gravediggers etc). Cities became more Estonian after industrialisation started to take off. During that time period local peasentry was freed from serfdom and thanks to industrialisation those peasents were able to become laborers in newly created factories. This pattern was common ammongst the towns that were given city rights before Russia conquered modern-day Estonia. Most of them were trading towns and that is why those towns had mainly Germans or otherwise non-Estonian population. During Russian rule Russia also created few administrative and later even few industrious towns. Most notably such towns were Võru and Paide (Võru gained and Paide regained it's city rights during rule of Catherine the Great). Because such towns didn't had historical precedent for German population, they ended up having mainly Estonian population even during 18th century.

Outside of cities, most Germans were landowners/manorholders and because of that they ended up living far away from each other in their castles or manors. That is why outside of cities there weren't any significant Germanic majority areas.

Most likely modern-day Latvia (except Latgale region) experienced similar situation as modern-day Estonia because both areas were under German jurisdiction and administration. This special status lasted until the beginning of the russification in the Baltic Provinces in 1876.

I don't know much about Lithuanian history and because of that I can't give an answer about the situation in Lithuania.

Hopefully my answer was helpful :)