Will importing the same statement twice create duplicates?

Not from our file: each transaction carries a stable id (the same statement in gives the same ids out), so QuickBooks recognises a second copy of our file. It cannot tell our copy of a transaction from the one your bank sent, so only convert months you have not already downloaded from the bank.

Which account does the upload go into?

In QuickBooks Online you pick the account during the upload.

Help

Import a converted statement into QuickBooks Online

QuickBooks Online takes a bank statement as a file upload. The simplest file to upload is the QuickBooks (.qbo) file from Convert, which is part of the $5 a month subscription. The free tier gives you a CSV, which QuickBooks Online also accepts once it has the columns Intuit asks for (below).

1. Make the .qbo file

On Convert, choose your statement (CSV or PDF). Check the preview and the line under each file: if money in shows as money out, click Flip signs. If the statement prints its opening and closing balances, the page also says whether the rows add up to them.
Under Download as, pick QuickBooks (.qbo).
Under Where should QuickBooks put it? choose New account in QuickBooks, say whether it is a bank account or a credit card statement, and pick the bank the statement came from. The converter asks for the bank on every .qbo file, because QuickBooks Desktop needs it; see the QuickBooks Desktop page for why.
If you already import this account's transactions from your bank, choose An account I already import into from my bank instead, and pick one .qbo file you downloaded from that bank.
Click Download QuickBooks (.qbo).

2. Upload it to QuickBooks Online

Open Bank transactions. In the newer QuickBooks layout it's under All apps → Accounting → Bank transactions.
Select the Link account dropdown, then Upload from file.
Choose the .qbo file, pick the QuickBooks account it belongs to, and follow the prompts.

Intuit's limits: files up to 350 KB and 1,000 transactions per upload. If you hit either one, convert fewer months at a time. Source: Intuit — Manually upload transactions into QuickBooks Online.

Uploading the free CSV instead

Intuit says a CSV upload should have 3 columns (Date, Description, Amount) or 4 (Date, Description, Credit, Debit). The converter's CSV has 6: Date, Description, Amount, Debit, Credit, Source file. Delete the columns you don't need in a spreadsheet first, or use the .qbo file, which is the simpler route.

Questions

Will importing the same statement twice create duplicates?: Not from our file: each transaction carries a stable id (the same statement in gives the same ids out), so QuickBooks recognises a second copy of our file. It cannot tell our copy of a transaction from the one your bank sent, so only convert months you have not already downloaded from the bank.
Which account does the upload go into?: In QuickBooks Online you pick the account during the upload.

Something else? Email support@avyth.com. A person reads it.