I think that there can be a couple of ways to interpret this. The first would be that on the most literal level, Isabel is chained to the Loyalist home of the Locktons. Being Loyalists, this is one nation to which Isabel is physically chained because she is a slave in their home. Yet, she might also be seen as chained to the hopes of the Patriot side. It is evident throughout the narrative that Isabel empathizes with the Patriotic cause because she views freedom for her own sense of being in the same light that the Patriots view it in their relationship with England. The "chained between two nations" could come to represent the physical bondage in which she is immersed in the Loyalist nation, but also can come to represent how she so strongly identifies with the Patriotic cause. These become the two nations to which she is physically and emotionally chained.
Another reading of this could be more introspective. On one hand, Isabel finds herself chained to the Patriotic cause and the cause of the newly conceived American nation. Yet, she also understands in the course of the narrative that the Patriotic cause is one that might not include the liberation of slavery. Isabel is perceptive enough to understand that the fight for the Patriotic conception of freedom does not apply to the slaves within the nation. The chaining that Isabel could speak of here reflects her desire to want freedom for the Patriots, as she identifies with their cause. Yet, she is equally chained to the idea that as a woman of color, slavery is not going to be abolished in the new nation. Hence, her chaining here consists of wanting freedom for the nation and for her own sense of self. Isabel can be seen as being chained between these two nations. In such an exploration, Anderson's development of Isabel's characterization is complex and intricate with regards to the issue of freedom and being "chained between two nations."